WO2016086320A1 - Tdp-43-binding polypeptides useful for the treatment of neurodegenerative diseases - Google Patents

Tdp-43-binding polypeptides useful for the treatment of neurodegenerative diseases Download PDF

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WO2016086320A1
WO2016086320A1 PCT/CA2015/051280 CA2015051280W WO2016086320A1 WO 2016086320 A1 WO2016086320 A1 WO 2016086320A1 CA 2015051280 W CA2015051280 W CA 2015051280W WO 2016086320 A1 WO2016086320 A1 WO 2016086320A1
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antigen
tdp
binding
construct
seq
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PCT/CA2015/051280
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French (fr)
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Jean-Pierre Julien
Claude Gravel
Silvia POZZI
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UNIVERSITé LAVAL
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Priority to US15/532,909 priority Critical patent/US10202443B2/en
Priority to EP15864525.9A priority patent/EP3227330B1/en
Priority to AU2015358266A priority patent/AU2015358266A1/en
Priority to JP2017529766A priority patent/JP6882172B2/en
Publication of WO2016086320A1 publication Critical patent/WO2016086320A1/en
Priority to AU2021250947A priority patent/AU2021250947A1/en

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    • A61P25/28—Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
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Definitions

  • TDP43 TAR DNA-binding protein of 43 kDA
  • the application also relates to methods of using the TDP-43 -binding polypeptides in the diagnosis and treatment of diseases characterized by TDP-43 proteinopathy such as amyotrophic lateral sclerosis, Azheimer's disease, motor neuron disease, Parkinson's disease and frontotemporal lobar degeneration.
  • TDP-43 proteinopathy such as amyotrophic lateral sclerosis, Azheimer's disease, motor neuron disease, Parkinson's disease and frontotemporal lobar degeneration.
  • Neurodegenerative diseases are characterized by selective neurodegeneration in specific regions of the brain and spinal cord.
  • Amyotrophic Lateral Sclerosis (ALS), commonly known as "Lou Gehrig's disease” is a progressive neurodegenerative disease of unknown etiology. The disease progressively impairs an individual's ability to control voluntary muscle movement. The disease tends to progress rapidly, leading to paralysis and death within 2-5 years of diagnosis in most cases.
  • TDP-43 A relatively recent discovery related to TDP-43 has provided fundamental insights into pathogenic mechanisms operative in ALS. TDP-43 was shown to be associated with the p65 sub-unit of the nuclear factor- ⁇ (NF- ⁇ ) inflammation-regulating transcription factor in spinal cord samples obtained from ALS patients, but not from spinal cord sample of control patients (V. Swamp et al., 2011, J. Exp. Med., 208:2429-2447).
  • NF- ⁇ nuclear factor- ⁇
  • antigen-binding constructs that bind to TDP-43 (TAR DNA- binding protein of 43 kDa), such as antibodies, including fragments, derivatives and variants.
  • the antigen-binding constructs specifically bind to the RRM- 1 domain of TDP-43.
  • the antigen-binding constructs when expressed in a cell, inhibits the binding of TDP-43 to the p65 subunit of NF- ⁇ in the cell by at least 5%, 10%, 20%, 30%, 40%, 50% 50%, 70%, 80%, or 90%.
  • the antigen-binding constructs when expressed in cells, attenuate the activation of NF- ⁇ in response to LPS in the cells by at least 5%, 10%, 20%, 30%, 40%, 50% 50%), 70%), 80%), or 90%.
  • the antigen-binding constructs, when expressed in a cell reduces the level of nuclear TDP-43 in the cell by at least 5%, 10%, 20%, 30%, 40%, 50% 50%, 70%, 80%, or 90%.
  • the antigen- binding constructs when expressed in ethacrynic acid-treated Hek293 cells, reduce TDP- 43 insolubility by at least 5%, 10%, 20%, 30%, 40%, 50% 50%, 70%, 80%, or 90%.
  • the antigen -binding constructs when expressed in Hek 293 cells incubated with TNF alpha, reduce the level of lysine acetylation of cellular TDP-43 by at least 5%, 10%, 20%, 30%, 40%, 50% 50%, 70%, 80%, or 90%.
  • antigen-binding constructs that specifically bind to TDP-43 comprising at least one complementarity determining region (CDR) selected from the amino acid sequences set forth in (SEQ ID NO: 7), (SEQ ID NO: 8), (SEQ ID NO: 9), (SEQ ID NO: 10), (SEQ ID NO: 1 1), (SEQ ID NO: 12), (SEQ ID NO: 12), (SEQ ID NO: 14), (SEQ ID NO: 15), (SEQ ID NO: 16), (SEQ ID NO: 17), (SEQ ID NO: 18), (SEQ ID NO: 19), (SEQ ID NO: 20), (SEQ ID NO: 21), (SEQ ID NO: 22), (SEQ ID NO: 23) and (SEQ ID NO: 24).
  • CDR complementarity determining region
  • antigen-binding constructs that specifically bind to TDP- 43 comprising at least one heavy chain variable region VH comprising three VH complementarity determining regions (CDRs), wherein the VH comprises one, two or three of :
  • a CDR selected from E6 VH1 CDR1, E6 VH7 CDR1, C10 VH3 CDR1 or C10 VH4 CDR1;
  • a CDR selected from E6 VH1 CDR3, E6 VH7 CDR3, C10 VH3 CDR3 or C10 VH4 CDR3.
  • the antigen-binding construct comprises one, two or three VH CDRs that are at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to these VH CDRs.
  • the antigen-binding construct comprises the VH region of E6 VH1, E6 VH7, C10 VH3 or C10 VH4, or a VH region that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the VH of E6 VH1, E6_VH7, C10_VH3 or C10_VH4.
  • the antigen-binding construct further comprise a variable light chain region VL, wherein the VL comprises three VL CDRs, and wherein the VL comprises one, two or three of:
  • a CDR selected from E6_VK9 CDRl and C 10_VK3 CDRl ;
  • the antigen-binding construct comprises the VL of E6_VK9 or C10_VK3, or an antigen-binding construct having a VL that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the VL of E6_VK9 or C 10_VK3.
  • the antigen binding construct comprises the VH region of E6 VH1 or E6 VH7 and the VL region of E6_VK9. In other embodiments, the antigen binding construct comprises the VH region of C10 VH3 or C10 VH4 and the VL region of C10_VK3. In other embodiments, the antigen-binding construct comprises the VH of E6 VH7 and the VL of E6_VK9, the VH of E6 VH1 and the VL of E6_VK9, the VH of C 10 VH3 and the VL of C 10_VK3 , or the VH of C 10 VH4 and the VL of C 10_VK3. [0012] In some embodiments, the antigen-binding construct comprises a peptide linker between the VH and VL, optionally the amino acid sequence SSGGGGSGGGGSGGGGS.
  • the antigen-binding construct are E6_Vh7VK9, E6_Vhl VK9, C10_ VH3 VK3 or C10_ VH4VK3.
  • the antigen-binding constructs comprise the six CDRs of E6_VH7VK9. In some embodiments, the antigen-binding constructs comprise the six CDRs of E6_VhlVK9. In some embodiments, the antigen-binding constructs comprise the six CDRs of C10_VH3VK3. In some embodiments, the antigen-binding constructs comprise the six CDRs of C10_VH4VK3.
  • the TDP-43 antigen-binding construct comprises a secretory signal peptide.
  • the secretory signal peptide is M G D N D I H F A F L S T G V H S Q V Q.
  • the TDP-43 antigen-binding construct have an scFv format.
  • the TDP-43 antigen-binding constructs have an Fab format.
  • the TDP-43 antigen binding construct has a single domain antibody (camelid) format.
  • the TDP-43 antigen-binding construct has an (Fab') 2 format.
  • the TDP-43 antigen-binding constructs may also comprise an Fc domain.
  • the antigen-binding constructs may also be humanized, or de-immunized.
  • antigen-binding constructs that specifically bind to an RRM-1 domain of TDP-43, comprising a VH and a VL, such that the construct, when expressed in cells, reduces the interaction of an intracellular TDP-43 polypeptide with an intracellular F- ⁇ p65 polypeptide, and/or reduces the activation of NF- ⁇ in cells in response to LPS.
  • the interaction of intracellular TDP-43 polypeptide with intracellular NF- ⁇ p65 polypeptide is reduced 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% or more.
  • the activation of F- KB in cells in response to LPS is reduced by 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% or more.
  • an antigen-binding construct that blocks by 50%, 60%, 70%, 80% or 90% or more the binding of any of E6_VHlVk9, E6_VH7Vk9, C10_VH3Vk3 or C10_VH4Vk3 to either TDP-43 or to the RRM-1 domain of TDP-43.
  • compositions comprising the antigen- binding construct described above, and pharmaceutically acceptable excipient.
  • AAV adeno-associated viral
  • antigen-binding constructs as defined herein for the manufacture of a medicament for the treatment or prevention of a disease or disorder characterized by TDP-proteinopathy.
  • the disease or disorder being treated is amyotrophic lateral sclerosis (ALS), Alzheimer's disease, motor neuron disease, Parkinson's disease, frontotemperal lobar degeneration (FTLD), mild cognitive impairment (MCI), Lewy body disease, brain trauma or cerebral ischemia.
  • ALS amyotrophic lateral sclerosis
  • FTLD frontotemperal lobar degeneration
  • MCI mild cognitive impairment
  • Lewy body disease brain trauma or cerebral ischemia.
  • Also provided are methods of producing the antigen-binding constructs comprising culturing a host cell under conditions suitable for expressing the antigen-binding construct, wherein the host cell comprises a polynucleotide encoding a TDP-43 antigen binding construct, and purifying the construct.
  • polynucleotide or set of isolated polynucleotides comprising at least one nucleic acid sequence that encodes at least one of the TDP-43 antigen-binding constructs.
  • the polynucleotide is a cDNA.
  • vector or set of vectors comprising one or more of the polynucleotides or sets of polynucleotides encoding the antigen-binding constructs.
  • the vector is a plasmid, a viral vector, a non-episomal mammalian vector, an expression vector, and a recombinant expression vector.
  • the vector is an adeno-associated viral (AAV) vector.
  • AAV adeno-associated viral
  • an isolated host cell comprising one or more polynucleotides encoding TDP-43 antigen binding constructs.
  • Figure 1 is an immunoblot of nuclear extracts of BV-2 cells that were fractionated by SDS-PAGE and treated with three exemplary monocloncal anti-TDP-43 antibodies, CIO, G8 and E6, raised against the RRMI domain of TDP-43.
  • the three antibodies detected TDP-43 in nuclear extracts of BV-2 cells that were stimulated with LPS or not.
  • Figure 2 is a bar graph showing the results of an ELISA assay demonstrating that human recombinant p65_His-Tag directly interacts with human recombinant TDP-43 GST Tag. The results are shown as the Absorbance (ABS) at 450 nm read for varying concentrations amount of human recombinant TDP-43 added to the assay from 0.01 to 0.8
  • Figure 3 is a bar graph showing the results of an ELISA assay demonstrating that interaction between recombinant TDP-43 and F- ⁇ p65 is blocked by exemplary monoclonal anti-TDP-43 antibodies CIO, G8, and E6. The results are shown as the Absorbance (ABS) at 450 nm read for the different recombinant anti-TDP-43 antibodies.
  • Figure 4 is a schematic representation of vectors encoding exemplary anti-TDP-43 scFv antibodies.
  • the scFv vectors were constructed in a VH-linker-VK format together with a flexible 20-amino acid linker (Gly4Ser)3.
  • the scFv constructs contain a murine immunoglobulin (Ig) ⁇ -secretory signal for efficient secretion and a human c-myc epitope 5 to facilitate detection.
  • Figure 5 is an immunoblot of an SDS PAGE gel of nuclear and cytoplasmic fractions of Hek293 cells transfected with an ScFv9 expression plasmids encoding anti- TDP-43 antigen-binding constructs E6 VH1 VK9 and E6_VH7VK9.
  • Figure 6 is a dot blot showing that the E6_VH1VK9 and E6_VH7VK9 antigeni c) binding constructs bind to amino acids 1-206 of TDP-43.
  • Figure 7 shows the results of an ELISA assay demonstrating that exemplary anti- TDP-43 antibodies E6_VH1VK9 and E6_VH7VK9 having an scFv format block the interaction between recombinant TDP-43 and F- ⁇ p65.
  • Figure 8 shows that an exemplary anti-TDP-43 antibody E6_VH1VK9 in an scFv 15 format co-immunoprecipitate with TDP-43 as detected by polyclonal antibodies against TDP-43. (expressed into the medium of Hek293 cells following transfection with ScFv9 expression plasmids encoding E6 VH1 VK9).
  • FIG. 9 shows that exemplary anti-TDP-43 antibody E6_VH1VK9 having an scFv format blocks the interaction of TDP-43 with NF- ⁇ p65 in Hek293 cells. This was 0 revealed by an assay in which cell extracts from Hek293 cells expressing E6_VH1VK9 were immunoprecipitated with anti-TDP-43 polyclonal antibodies, revealing a decreased level of NF- ⁇ p65 for cells expressing VHl VK9 compared to cells transfected with an empty ScFv9 expression vector.
  • Figure 10 shows the ability of expression vectors encoding exemplary scFv 5 antibodies against TDP-43 to attenuate NF- ⁇ activity in response to LPS as measured by a NF-KB -luciferase reporter construct stably integrated into BV2 microglial cells.
  • Figure 11 shows the reduction in levels of nuclear TDP-43 caused by expression of scFv anti-TDP-43 antibodies in Neuro2A cells.
  • Figure 12 shows the ability of anti-TDP-43 antibody to reduce TDP-43 insolubility in E6_VH1VK9 and E6_VH7VK9 transfected Hek293 cells treated with ethacrynic acid.
  • A shows a western blot.
  • B shows a dot blot analysis.
  • Figure 13 shows the ability of anti-TDP-43 antibodies to protect TDP-43 from lysine acetylation in E6 VH1 VK9 and E6_VH7VK9 transfected Hek293 cells.
  • TDP-43 -binding constructs and their uses in the diagnosis and therapy of neurodegenerative diseases characterized by TDP-43 proteinopathy.
  • TDP43 refers to transactivation responsive-DNA binding protein of 43kDa, or TAR-DNA binding protein of 43kDA, and is used to refer to all types and forms of TPD-43, including the native form as well as other conform ers of TDP- 43, including for example, phosphorylated forms of TDP-43, aggregates of TDP-43, ubiquitin-associated aggregates of TDP-43 and TDP-43 variants that have one or more mutations compared to native TDP-43, and pathogenic forms.
  • TDP-43 also includes fragments of TDP-43 polypeptide.
  • TDP-43 is a DNA/RNA-binding protein that contains an N-terminal domain, two RNA-recognition motifs and a glycine-rich C-terminal domain thought to be important for mediating protein-protein interactions
  • the amino acid sequence of human TDP-43 is known in the art; see, e.g., Strausberg et al., TARDBP protein (Homo sapiens) GenBank Pubmed: An amino acid sequence of human TDP 43 is shown in AAH71657 version GL47939520 herein incorporated by reference in its entirety.
  • the amino acid sequence of native human TDP-43 is as shown below and in Table A (SEQ ID NO: 29).
  • the RRMl domain corresponds to amino acids 101 to 176.
  • FkB p65 or FKB refers to nuclear factor kappa B
  • NF-kB p65 or “p65” are used interchangeably herein to refer to the p65 subunit or chain of NFkB p65.
  • p65 polypeptides as well as polynucleotides are known in the art. For example see NCBI M62399.1. An amino acid sequence for human NF- ⁇ p65 is shown below. Reference to p65 herein also includes fragments of p65.
  • TDP-43 proteinopathy relates to the nervous system diseases, in particular to neurodegenerative diseases, and are known as a heterologous group of disorders linked by association with TDP-43 abnormalities, and particularly with accumulation and/or aggregation of abnormal or misfolded TDP-43 polypeptides.
  • TDP proteinopathies include, but are not limited to amyotrophic lateral sclerosis (ALS), Parkinson's disease, frontotemporal lobar degeneration (FTLD) motor neuron disease, Alzheimer's disease, dementia with Lewy bodies, Huntington's disease, or Lewy body disease.
  • Abnormal TDP-43 accumulations may also be triggered by nerve injury, brain trauma, brain ischemia (stroke).
  • Frontotemporal lobar degeneration disease refers to a group of disorders associated with atrophy in the frontal and temporal lobes.
  • Frontotemporal lobar degeneration disease can include FTLD-tau characterized by tau inclusion, FTLD- TDP43 characterized by ubiquitin and TDP-43 inclusion (FTLD-U), FTLD-FUS characterized by FUS cytoplasmic inclusions and dementia lacking distinctive histology (DLDH).
  • FTLD-tau FTLD-tau characterized by tau inclusion
  • FTLD- TDP43 characterized by ubiquitin and TDP-43 inclusion
  • FTLD-FUS characterized by FUS cytoplasmic inclusions and dementia lacking distinctive histology
  • DLDH amyotrophic lateral sclerosis
  • ALS amyotrophic lateral sclerosis
  • antigen-binding constructs that bind to TDP-43 (TAR DNA- binding protein of 43 kDa), such as antibodies, including fragments, derivatives and variants of antibodies that are capable of specifically binding to TDP-43.
  • TDP-43 TAR DNA- binding protein of 43 kDa
  • antibodies including fragments, derivatives and variants of antibodies that are capable of specifically binding to TDP-43.
  • TDP-43 antibody specifically, generally, and collectively, antibodies to TDP- 43, or misfolded or oligomeric or aggregated or posttranslationally modified TDP-43 or variants of TDP-43.
  • antibodies as described herein specifically binds to the RRM-1 domain of TDP- 43.
  • the TDP-43 specific antigen binding construct is an antibody (including antigen-binding fragments or derivatives thereof) having an immunological binding characteristic of the antibodies described herein.
  • the antigen-binding constructs block the binding of TPD-43 to NF-KB p65.
  • antigen-binding constructs that specifically bind to TDP-43 comprising at least one heavy chain variable region VH comprising three VH complementarity determining regions (CDRs), wherein the VH comprises one, two or three of:
  • a CDR selected from E6 VH1 CDR1, E6 VH7 CDR1, C10 VH3 CDR1 or C10 VH4 CDR1;
  • a CDR selected from E6 VH1 CDR3, E6 VH7 CDR3, C10 VH3 CDR3 or C10 VH4 CDR3.
  • the antigen-binding construct comprises one, two or three VH CDRs that are at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the those VH CDRs.
  • the antigen-binding construct comprises the VH of E6 VH1, E6_VH7, C10_VH3 or C10_VH4, or a VH that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the VH of E6 VH1, E6_VH7, C10_VH3 or C10 VH4.
  • the antigen-binding construct of of further comprising a variable light chain region VL, wherein the VL comprises three VL CDRs, and wherein the VL comprises one, two or three of:
  • a CDR selected from E6_VK9 CDR2 and C10_VK3 CDR2 and/or ⁇ a CDR selected from E6_VK9 CDR3 or C 10_VK3 CDR3 ; as well as antigen-binding constructs comprising a CDR that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to those VL CDRs.
  • the antigen-binding construct comprises the VL of E6_VK9 or C10_VK3, or an antigen-binding construct having a VL that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the VL of E6 VK9 or C10 VK3.
  • the antigen binding construct comprises the VH region of E6 VH1 or E6 VH7 and the VL region of E6_ VK9.
  • the antigen binding construct comprises the VH region of C10 VH3 or C10 VH4 and the VL region of C10_ VK3.
  • the antigen-binding construct comprises the VH of E6 VH7 and the VL of E6_VK9, the VH of E6 VH1 and the VL of E6_VK9, the VH of C 10 VH3 and the VL of C 10_VK3 , or the VH of C 10 VH4 and the VL of C 10_ VK3.
  • the antigen-binding construct comprises the six CDRs selected from:
  • the antigen-binding construct comprises a peptide linker between the VH and VL, optionally the amino acid sequence SSGGGGSGGGGSGGGGS.
  • the antigen-binding construct comprises E6_Vh7VK9, E6_VhlVK9, C10_VH3VK3 or C10_VH4VK3.
  • the antigen-binding construct comprises a secretory signal peptide.
  • the secretory signal peptide is M G D N D I H F A F L S T G V H S Q V Q.
  • the antigen-binding construct have an scFv format.
  • the antigen-binding constructs have an Fab format.
  • the antigen binding construct has a single domain antibody (for example, a camelid) format.
  • the antigen-binding construct has an (Fab') 2 format.
  • the antigen-binding construct has an Fab' format.
  • the antigen-binding constructs may also comprise an Fc domain.
  • the antigen-binding constructs may also be humanized, or de-immunized.
  • antigen-binding constructs that specifically bind to an RRM-1 domain of TDP-43, comprising a VH and a VL, such that the construct, when expressed in cells, reduces the interaction of an intracellular TDP-43 polypeptide with an intracellular F- ⁇ p65 polypeptide and/or reduces the activation of NF- ⁇ in cells in response to LPS.
  • the interaction of intracellular TDP-43 polypeptide with intracellular F- ⁇ p65 polypeptide is reduced 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% or more.
  • the activation of F- KB in cells in response to LPS is reduced by 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% or more.
  • antigen-binding constructs that specifically bind to an RRM-1 domain of TDP-43, comprising a VH and a VL, wherein the construct, when expressed in a cell, i) reduces the interaction of an intracellular TDP-43 polypeptide with an intracellular F- ⁇ p65 polypeptide in Hek293 cells by 10% or more; or
  • iii) reduces the level of nuclear TDP-43 in Neuro2A cells; or iv) reduces the lysine acetylation of TDP-43 in Hek293 cells in response to TNF alpha by 10% or more; or v) reduces the insolubility of TDP-43 in Hek293 cells incubated with ethacrynic acid.
  • antigen-binding construct that blocks by 50%, 60%, 70%, 80% or 90% or more the binding of any of E6_VHlVk9, E6_VH7Vk9, C10_VH3Vk3 or C10_VH4Vk3 to either TDP-43 or to the RRM-1 domain of TDP-43.
  • the antigen-binding construct blocks the binding of any of E6 VH1 Vk9, E6_VH7Vk9, C10_VH3Vk3 or C10_VH4Vk3 to either TDP-43 or to the RRM-1 domain of TDP-43 by 50% or more.
  • an antigen binding construct also refers to any agent, e.g., polypeptide or polypeptide complex capable of binding to an antigen.
  • an antigen binding construct is a polypeptide the specifically binds to an antigen of interest.
  • An antigen binding construct can be a monomer, dimer, multimer, a protein, a peptide, or a protein or peptide complex; an antibody, an antibody fragment, or an antigen binding fragment thereof; an scFv and the like.
  • An antigen binding construct can be a polypeptide construct that is monospecific, bispecific, or multispecific.
  • an antigen binding construct can include, e.g., one or more antigen binding components (e.g., Fabs or scFvs) linked to one or more Fc. Further examples of antigen binding constructs are described below and provided in the Examples.
  • bispecific is intended to include any agent, e.g., an antigen binding construct or antibody, which has two different binding specificities.
  • multispecific or “heterospecific” is intended to include any agent, e.g., an antigen binding construct or antibody, which has two or more different binding specificities. Accordingly, embodiments of the antigen-binding constructs described herein, are inclusive of, but not limited to, bispecific, trispecific, tetraspecific, and other multispecific molecules.
  • an antigen binding construct can be an antibody or antigen binding portion thereof.
  • an "antibody” or “immunoglobulin” refers to a polypeptide substantially encoded by an immunoglobulin gene or immunoglobulin genes, or fragments thereof, which specifically bind and recognize an analyte (e.g., antigen).
  • the recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as the myriad immunoglobulin variable region genes.
  • Light chains are classified as either kappa or lambda.
  • the "class" of an antibody or immunoglobulin refers to the type of constant domain or constant region possessed by its heavy chain.
  • IgA immunoglobulin
  • IgD immunoglobulin
  • IgE immunoglobulin
  • IgG immunoglobulin
  • IgM immunoglobulins
  • An exemplary immunoglobulin (antibody) structural unit is composed of two pairs of polypeptide chains, each pair having one "light” (about 25 kD) and one "heavy” chain (about 50-70 kD).
  • the N-terminal domain of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition.
  • the terms variable light chain (VL) and variable heavy chain (VH) refer to these light and heavy chain domains respectively.
  • the IgGl heavy chain comprises the VH, CHI, CH2 and CH3 domains respectively from the N to C-terminus.
  • the light chain comprises the VL and CL domains from N to C terminus.
  • the IgGl heavy chain comprises a hinge between the CHI and CH2 domains.
  • the immunoglobulin constructs comprise at least one immunoglobulin domain from IgG, IgM, IgA, IgD, or IgE connected to a therapeutic polypeptide.
  • the immunoglobulin domain found in an antigen binding construct provided herein is from or derived from an immunoglobulin based construct such as a diabody, or a nanobody.
  • the immunoglobulin constructs described herein comprise at least one immunoglobulin domain from a heavy chain antibody such as a camelid antibody.
  • the immunoglobulin constructs provided herein comprise at least one immunoglobulin domain from a mammalian antibody such as a bovine antibody, a human antibody, a camelid antibody, a mouse antibody or any chimeric antibody.
  • a mammalian antibody such as a bovine antibody, a human antibody, a camelid antibody, a mouse antibody or any chimeric antibody.
  • HVR hypervariable region
  • native four-chain antibodies comprise six HVRs; three in the VH (HI, H2, H3), and three in the VL (LI, L2, L3).
  • HVRs generally comprise amino acid residues from the hypervariable loops and/or from the complementarity determining regions (CDRs), the latter being of highest sequence variability and/or involved in antigen recognition. With the exception of CDR1 in VH, CDRs generally comprise the amino acid residues that form the hypervariable loops.
  • CDRs complementarity determining regions
  • Hypervariable regions (HVRs) are also referred to as "complementarity determining regions” (CDRs), and these terms are used herein interchangeably in reference to portions of the variable region that form the antigen binding regions. This particular region has been described by Kabat et al., U.S. Dept.
  • An "Fab molecule” or a “Fab” refers to a protein or polypeptide construct consisting of the VH and CHI domain of the heavy chain (the “Fab heavy chain”) and the VL and CL domain of the light chain (the “Fab light chain”) of an immunoglobulin.
  • a Fab is monovalent.
  • An “F(ab') 2 " molecule refers to a protein or polypeptide construct consisting of two Fabs linked together by part of a hinge region, but is missing the most of the Fc.
  • An F(ab') 2 molecule may be obtained by digesting an immunoglobulin with papain or pepsin.
  • single-chain refers to a molecule comprising amino acid monomers linearly linked by peptide bonds.
  • one of the antigen binding moieties is a single-chain Fab molecule, i.e. a Fab molecule wherein the Fab light chain and the Fab heavy chain are connected by a peptide linker to form a single peptide chain.
  • the C-terminus of the Fab light chain is connected to the N-terminus of the Fab heavy chain in the single-chain Fab molecule.
  • one of the antigen binding moieties is a single-chain Fv molecule (scFv).
  • an "scFv” has a variable domain of light chain (VL) connected from its C-terminus to the N-terminal end of a variable domain of heavy chain (VH) by a polypeptide chain, or alternately the the C-terminal end of the VH is connected to the N-terminal end of VL by a polypeptide chain.
  • Antibodies of this type are referred to herein as having an "scFv format”.
  • an scFv format is used in an antigen- binding construct (i.e. antigen -binding domains composed of a heavy chain variable domain and a light chain variable domain).
  • said scFv molecules are human.
  • said scFv molecules are humanized.
  • said scFv molecules are murine.
  • the variable regions may be connected directly or, typically, via a linker peptide that allows the formation of a functional antigen-binding moiety. Typical peptide linkers comprise about 2-20 amino acids, and are described herein or known in the art.
  • Suitable, non-immunogenic linker peptides include, for example, (G4S)n, (SG4)n, (G4S)n, G4(SG4)n or G2(SG2)n linker peptides, wherein n is generally a number between 1 and 10, typically between 2 and 4.
  • the scFv molecule may be further stabilized by disulfide bridges between the heavy and light chain variable domains, for example as described in Reiter et al. (Nat Biotechnol 14, 1239-1245 (1996)).
  • scFvs can also be stabilized by mutation of CDR sequences, as described in [Miller et al., Protein Eng Des Sel.
  • an TDP-43 antigen-binding construct in an scFv format is preferred for its ability to cross cell membranes and enter cells.
  • a schematic representation of an scFv format antibody is shown in Figure 4B.
  • a TDP-43 antigen-binding construct may consist of a single VH polypeptide (camelid format).
  • crossover Fab molecule also termed “Crossfab”
  • the crossover Fab molecule comprises a peptide chain composed of the light chain variable region and the heavy chain constant region, and a peptide chain composed of the heavy chain variable region and the light chain constant region.
  • the peptide chain comprising the heavy chain constant region is referred to herein as the "heavy chain” of the crossover Fab molecule.
  • the peptide chain comprising the heavy chain variable region is referred to herein as the "heavy chain" of the crossover Fab molecule.
  • FR refers to variable domain residues other than hypervariable region (HVR) residues.
  • the FR of a variable domain generally consists of four FR domains: FR1 , FR2, FR3, and FR4. Accordingly, the HVR and FR sequences generally appear in the following sequence in VH (or VL): FR1-H1(L1)-FR2-H2(L2)-FR3-H3(L3)- FR4.
  • the antigen-binding constructs may comprise an Fc region or domain, e.g., a dimeric Fc.
  • Fc domain or "Fc region” herein is used to define a C-terminal region of an immunoglobulin heavy chain that contains at least a portion of the constant region.
  • the term includes native sequence Fc regions and variant Fc regions. Unless otherwise specified herein, numbering of amino acid residues in the Fc region or constant region is according to the EU numbering system, also called the EU index, as described in Kabat et al, Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD, 1991.
  • a "subunit" of an Fc domain as used herein refers to one of the two polypeptides forming the dimeric Fc domain, i.e. a polypeptide comprising C-terminal constant regions of an immunoglobulin heavy chain, capable of stable self-association.
  • a subunit of an IgG Fc domain comprises an IgG C H2 and an IgG C H3 constant domain.
  • the Fc comprises at least one or two C H3 sequences.
  • the Fc is a homodimeris Fc.
  • the Fc is heterodimeric FC.
  • the Fc is a human Fc.
  • the Fc is a murine Fc.
  • the Fc is a human IgG or IgGl Fc.
  • the Fc comprises at least one or two C H2 sequences.
  • the Fc comprises one or more modifications in at least one of the C H3 sequences. In some aspects, the Fc comprises one or more modifications in at least one of the C H2 sequences. In some aspects, an Fc is a single polypeptide. In some aspects, an Fc is multiple peptides, e.g., two polypeptides.
  • Fused or linked means that the components (e.g. a Fab molecule or an scFv molecule and an Fc domain subunit) are linked by peptide bonds, either directly or via one or more peptide linkers.
  • Antigen-binding constructs bind antigen.
  • antigenic determinant is synonymous with “antigen” and “epitope,” and refers to a site (e.g. a contiguous stretch of amino acids or a conformational configuration made up of different regions of non-contiguous amino acids) on a polypeptide macromolecule to which an antigen-binding moiety binds, forming an antigen-binding moiety-antigen complex.
  • the antigen bound by the antigen-binding constructs described herein is TPD-43, and in some embodiments, the RRM-1 domain of TDP-43.
  • binds means that the binding is selective for the antigen and can be discriminated from unwanted or non-specific interactions.
  • the ability of an antigen-binding moiety to bind to a specific antigenic determinant can be measured either through an enzyme-linked immunosorbent assay (ELISA) or other techniques familiar to one of skill in the art, e.g. surface plasmon resonance (SPR) technique (analyzed on a BIAcore instrument) (Liljeblad et al, Glyco J 17, 323-329 (2000)), and traditional binding assays (Heeley, Endocr Res 28, 217-229 (2002)).
  • ELISA enzyme-linked immunosorbent assay
  • SPR surface plasmon resonance
  • an antigen-binding moiety that binds to the antigen, or an antigen-binding molecule comprising that antigen-binding moiety has a dissociation constant (K D ) of ⁇ 1 ⁇ , ⁇ 100 nM, ⁇ 10 nM, ⁇ 1 nM, ⁇ 0.1 nM, ⁇ 0.01 nM, or ⁇ 0.001 nM (e.g. 10 ⁇ 8 M or less, e.g.
  • An antibody "which binds" an antigen of interest is one capable of binding that antigen with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent.
  • Binding affinity refers to intrinsic binding affinity which reflects a 1 : 1 interaction between members of a binding pair (e.g., an antigen-binding construct and an antigen, or a receptor and its ligand).
  • the affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (K D ), which is the ratio of dissociation and association rate constants (k 0ff and k on , respectively).
  • affinities may comprise different rate constants, as long as the ratio of the rate constants remains the same.
  • Affinity can be measured by well-established methods known in the art, including those described herein.
  • a particular method for measuring affinity is Surface Plasmon Resonance (SPR).
  • the antigen-binding constructs described herein include at least one antigen- binding polypeptide that binds TDP-43.
  • Table A shows the amino acid sequences of exemplary anti-TDP-43 antigen binding polypeptides.
  • nucleic acid sequences encoding the exemplary antigen- binding constructs Table B shows these exemplary nucleic acid sequences.
  • E6_VH1VK9 complete (MGDNDIHFAFLSTGVHSOVO! LOESGGGLVOPGG with IGk secretory S Met KLSCVASGFTSSNYWLNWVRQSPERGLE
  • E6_VH7VK9 complete fMGDNDIHFAFLSTGVHSOVO! LQQS G G G LVQ P G with IGk secretory G S Met KLS CVAS G FTSS N YWL NWVRQS P E RG signal and c-myc L EWVA E I R L KS N N YAT NYA E SVKG R F TI S RD peptide DS KS SVY LQVN N L RA E DTG I YYCTRSTA RAT
  • E6_VH1VK9 clone atgggtgacaatgacatccactttgcctttctctccacaggtgtccactcccaggtccaCTGCAGG complete with Igk AGTCTGGAGGAGGCTTGGTGCAACCTGGAGGATCCATGAAACTCTCCTGTGT
  • E6_VH7VK9 atgggtgacaatgacatccactttgcctttctctccacaggtgtccactcccaggtccaCTGCAGC clone complete with Igk AGTCTGGAGGAGGCTTGGTGCAACCTGGAGGATCCATGAAACTCTCCTGTGT
  • the antigen-binding constructs described herein comprise at least one TDP-43- binding polypeptide. Also described are polynucleotides encoding the TDP-43 -binding polypeptides described herein.
  • isolated means an agent (e.g., a polypeptide or polynucleotide) that has been identified and separated and/or recovered from a component of its natural cell culture environment. Contaminant components of its natural environment are materials that would interfere with diagnostic or therapeutic uses for the antigen-binding construct, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. Isolated also refers to an agent that has been synthetically produced, e.g., via human intervention. [0086] The terms "polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues.
  • a description directed to a polypeptide applies equally to a description of a peptide and a description of a protein, and vice versa.
  • the terms apply to naturally occurring amino acid polymers as well as amino acid polymers in which one or more amino acid residues is a non-naturally encoded amino acid.
  • the terms encompass amino acid chains of any length, including full length proteins, wherein the amino acid residues are linked by covalent peptide bonds.
  • amino acid refers to naturally occurring and non-naturally occurring amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids.
  • Naturally encoded amino acids are the 20 common amino acids (alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, praline, serine, threonine, tryptophan, tyrosine, and valine) and pyrrolysine and selenocysteine.
  • Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, such as, homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium.
  • Such analogs have modified R groups (such as, norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid.
  • Reference to an amino acid includes, for example, naturally occurring proteogenic L-amino acids; D-amino acids, chemically modified amino acids such as amino acid variants and derivatives; naturally occurring non -proteogenic amino acids such as ⁇ -alanine, ornithine, etc.; and chemically synthesized compounds having properties known in the art to be characteristic of amino acids.
  • non-naturally occurring amino acids include, but are not limited to, oc- methyl amino acids (e.g.
  • oc-methyl alanine D-amino acids
  • histidine-like amino acids e.g., 2-amino-histidine, ⁇ -hydroxy-histidine, homohistidine
  • amino acids having an extra methylene in the side chain (“homo" amino acids)
  • amino acids having an extra methylene in the side chain (“homo” amino acids)
  • amino acids having an extra methylene in the side chain (“homo” amino acids)
  • amino acids in which a carboxylic acid functional group in the side chain is replaced with a sulfonic acid group e.g., cysteic acid.
  • the incorporation of non-natural amino acids, including synthetic non-native amino acids, substituted amino acids, or one or more D-amino acids into the proteins as described herein may be advantageous in a number of different ways.
  • D-amino acid-containing peptides, etc. exhibit increased stability in vitro or in vivo compared to L-amino acid- containing counterparts.
  • the construction of peptides, etc., incorporating D-amino acids can be particularly useful when greater intracellular stability is desired or required.
  • D-peptides, etc. are resistant to endogenous peptidases and proteases, thereby providing improved bioavailability of the molecule, and prolonged lifetimes in vivo when such properties are desirable.
  • D-peptides, etc. cannot be processed efficiently for major histocompatibility complex class II-restricted presentation to T helper cells, and are therefore, less likely to induce humoral immune responses in the whole organism.
  • Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
  • polynucleotides encoding polypeptides of the antigen-binding constructs.
  • polynucleotide or “nucleotide sequence” is intended to indicate a consecutive stretch of two or more nucleotide molecules.
  • the nucleotide sequence may be of genomic, cDNA, RNA, semisynthetic or synthetic origin, or any combination thereof.
  • nucleic acid refers to deoxyribonucleotides, deoxyribonucleosides, ribonucleosides, or ribonucleotides and polymers thereof in either single- or double- stranded form.
  • the term encompasses nucleic acids containing known analogues of natural nucleotides which have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless specifically limited otherwise, the term also refers to oligonucleotide analogs including PNA (peptidonucleic acid), analogs of DNA used in antisense technology (phosphorothioates, phosphoroamidates, and the like). Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (including but not limited to, degenerate codon substitutions) and complementary sequences as well as the sequence explicitly indicated.
  • degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)).
  • Constantly modified variants applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, “conservatively modified variants” refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide.
  • nucleic acid variations are "silent variations," which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid.
  • each codon in a nucleic acid except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan
  • TGG which is ordinarily the only codon for tryptophan
  • amino acid sequences one of ordinary skill in the art will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the deletion of an amino acid, addition of an amino acid, or substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are known to those of ordinary skill in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles as described herein.
  • Conservative substitution tables providing functionally similar amino acids are known to those of ordinary skill in the art.
  • the following eight groups each contain amino acids that are conservative substitutions for one another: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and [0139] 8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins: Structures and Molecular Properties (W H Freeman & Co.; 2nd edition (December 1993).
  • nucleic acids or polypeptide sequences refer to two or more sequences or subsequences that are the same. Sequences are "substantially identical” if they have a percentage of amino acid residues or nucleotides that are the same (i.e., about 60% identity, about 65%, about 70%, about 75%), about 80%>, about 85%, about 90%, or about 95% identity over a specified region), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms (or other algorithms available to persons of ordinary skill in the art) or by manual alignment and visual inspection.
  • This definition also refers to the complement of a test sequence.
  • the identity can exist over a region that is at least about 50 amino acids or nucleotides in length, or over a region that is 75-100 amino acids or nucleotides in length, or, where not specified, across the entire sequence of a polynucleotide or polypeptide.
  • a polynucleotide encoding a polypeptide as described herein, including homologs from species other than human, may be obtained by a process comprising the steps of screening a library under stringent hybridization conditions with a labeled probe having a polynucleotide sequence as described herein or a fragment thereof, and isolating full-length cDNA and genomic clones containing said polynucleotide sequence.
  • Such hybridization techniques are well known to the skilled artisan.
  • sequence comparison typically one sequence acts as a reference sequence, to which test sequences are compared.
  • sequence comparison algorithm test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated.
  • the sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
  • a “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
  • Methods of alignment of sequences for comparison are known to those of ordinary skill in the art.
  • Optimal alignment of sequences for comparison can be conducted, including but not limited to, by the local homology algorithm of Smith and Waterman (1970) Adv. Appl. Math. 2:482c, by the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol.
  • BLAST and BLAST 2.0 algorithms are described in Altschul et al. (1997) Nuc. Acids Res. 25:3389-3402, and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively.
  • Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information available at the World Wide Web at ncbi.nlm.nih.gov.
  • the BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment.
  • W wordlength
  • E expectation
  • B B-BLAST algorithm
  • E expectation
  • the BLAST algorithm is typically performed with the "low complexity" filter turned off.
  • the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873- 5787).
  • One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance.
  • P(N) the smallest sum probability
  • a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, or less than about 0.01, or less than about 0.001.
  • the phrase "selectively (or specifically) hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (including but not limited to, total cellular or library DNA or RNA).
  • stringent hybridization conditions refers to hybridization of sequences of DNA, RNA, or other nucleic acids, or combinations thereof under conditions of low ionic strength and high temperature as is known in the art. Typically, under stringent conditions a probe will hybridize to its target subsequence in a complex mixture of nucleic acid (including but not limited to, total cellular or library DNA or RNA) but does not hybridize to other sequences in the complex mixture. Stringent conditions are sequence- dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures.
  • engineered, engineered, engineering are considered to include any manipulation of the peptide backbone or the post-translational modifications of a naturally occurring or recombinant polypeptide or fragment thereof. Engineering includes modifications of the amino acid sequence, of the glycosylation pattern, or of the side chain group of individual amino acids, as well as combinations of these approaches.
  • the engineered proteins are expressed and produced by standard molecular biology techniques.
  • isolated nucleic acid molecule or polynucleotide is intended a nucleic acid molecule, DNA or RNA, which has been removed from its native environment.
  • a recombinant polynucleotide encoding a polypeptide contained in a vector is considered isolated.
  • Further examples of an isolated polynucleotide include recombinant polynucleotides maintained in heterologous host cells or purified (partially or substantially) polynucleotides in solution.
  • An isolated polynucleotide includes a polynucleotide molecule contained in cells that ordinarily contain the polynucleotide molecule, but the polynucleotide molecule is present extrachromosomally or at a chromosomal location that is different from its natural chromosomal location.
  • Isolated RNA molecules include in vivo or in vitro RNA transcripts, as well as positive and negative strand forms, and double- stranded forms.
  • Isolated polynucleotides or nucleic acids described herein further include such molecules produced synthetically, e.g., via PCR or chemical synthesis.
  • a polynucleotide or a nucleic acid in certain embodiments, include a regulatory element such as a promoter, ribosome binding site, or a transcription terminator.
  • PCR polymerase chain reaction
  • PCR generally refers to a method for amplification of a desired nucleotide sequence in vitro, as described, for example, in U.S. Pat. No. 4,683, 195.
  • the PCR method involves repeated cycles of primer extension synthesis, using oligonucleotide primers capable of hybridising preferentially to a template nucleic acid.
  • nucleic acid or polynucleotide having a nucleotide sequence at least, for example, 95% "identical" to a reference nucleotide sequence as described herein it is intended that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence.
  • a polynucleotide having a nucleotide sequence at least 95% identical to a reference nucleotide sequence up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence.
  • These alterations of the reference sequence may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.
  • polypeptide sequence is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a nucleotide sequence as described herein can be determined conventionally using known computer programs, such as the ones discussed above for polypeptides (e.g. ALIGN-2).
  • a derivative, or a variant of a polypeptide is said to share "homology" or be "homologous” with the peptide if the amino acid sequences of the derivative or variant has at least 50% identity with a 100 amino acid sequence from the original peptide.
  • the derivative or variant is at least 75% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In certain embodiments, the derivative or variant is at least 85% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In certain embodiments, the amino acid sequence of the derivative is at least 90% the same as the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In some embodiments, the amino acid sequence of the derivative is at least 95% the same as the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative.
  • the derivative or variant is at least 99% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative.
  • modified refers to any changes made to a given polypeptide, such as changes to the length of the polypeptide, the amino acid sequence, chemical structure, co-translational modification, or post-translational modification of a polypeptide.
  • the form "(modified)" term means that the polypeptides being discussed are optionally modified, that is, the polypeptides under discussion can be modified or unmodified.
  • an antigen-binding construct comprises an amino acids sequence that is at least 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identical to a relevant amino acid sequence or fragment thereof set forth in the Table(s) or accession number(s) disclosed herein.
  • an isolated antigen-binding construct comprises an amino acids sequence encoded by a polynucleotide that is at least 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identical to a relevant nucleotide sequence or fragment thereof set forth in Table(s) or accession number(s) disclosed herein.
  • the antigen-binding polypeptide is derived from humanized, or chimeric versions of these antibodies.
  • Humanized forms of non-human (e.g., rodent) antibodies are chimeric antibodies that contain minimal sequence derived from non-human immunoglobulin.
  • humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and capacity.
  • donor antibody such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and capacity.
  • framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non- human immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence.
  • the humanized antibody optionally also may comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
  • Fc immunoglobulin constant region
  • the anti-TDP-43 antigen binding constructs are humanized.
  • the humanized anti-TDP-43 antibodies comprise the amino acids of murine CDRs.
  • De-immunization can also be used to decrease the immunogemcity of an antibody.
  • the term "de-immunization” includes alteration of an antibody to modify T cell epitopes; see, e.g., international Application Publication Nos. W098/52976 and WO00/34317.
  • VH and VL sequences from the starting antibody are analyzed and a human T cell epitope "map" from each V region showing the location of epitopes in relation to complementarity determining regions (CDRs) and other key residues within the sequence.
  • CDRs complementarity determining regions
  • VH and VL sequences are designed comprising combinations of amino acid substitutions and these sequences are subsequently incorporated into a range of binding polypeptides, e.g., TDP-43 -specific antibodies, including immunospecific fragments thereof, for use in the diagnostic and treatment methods disclosed herein, which are then tested for function.
  • TDP-43 -specific antibodies e.g., TDP-43 -specific antibodies, including immunospecific fragments thereof, for use in the diagnostic and treatment methods disclosed herein, which are then tested for function.
  • TDP-43 -specific antibodies e.g., TDP-43 -specific antibodies, including immunospecific fragments thereof, for use in the diagnostic and treatment methods disclosed herein, which are then tested for function.
  • TDP-43 -specific antibodies e.g., TDP-43 -specific antibodies, including immunospecific fragments thereof, for use in the diagnostic and treatment methods disclosed herein, which are then tested for function.
  • compositions comprising an antigen- binding constructs described herein.
  • Such compositions comprise the construct and a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.
  • carrier refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic is administered.
  • Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like.
  • the carrier is a man-made carrier not found in nature.
  • Water can be used as a carrier when the pharmaceutical composition is administered intravenously.
  • Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions.
  • Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like.
  • the composition if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents.
  • compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like.
  • the composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides.
  • Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical carriers are described in "Remington's Pharmaceutical Sciences" by E. W. Martin.
  • Such compositions will contain a therapeutically effective amount of the compound, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient.
  • the formulation should suit the mode of administration.
  • the composition comprising the construct is formulated in accordance with routine procedures as a pharmaceutical composition adapted for intravenous administration to human beings.
  • compositions for intravenous administration are solutions in sterile isotonic aqueous buffer.
  • the composition may also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection.
  • the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent.
  • composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline.
  • an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.
  • compositions described herein are formulated as neutral or salt forms.
  • Pharmaceutically acceptable salts include those formed with anions such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with cations such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxide isopropyl amine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.
  • the antigen-binding constructs are produced as recombinant molecules by expression in a cell, e.g., yeast, a microorganism such as a bacterium, or a human or animal cell line.
  • the anti-TDP-43 antigen- binding constructs are secreted from the cells.
  • the antigen-binding constructs can be expressed in a host cell using an expression cassette coding for the antigen-binding construct.
  • expression cassette refers to a polynucleotide generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a target cell.
  • the recombinant expression cassette can be incorporated into a vector, e.g., a plasmid, chromosome, mitochondrial DNA, plastid DNA, virus, or nucleic acid fragment.
  • the recombinant expression cassette portion of an expression vector includes, among other sequences, a nucleic acid sequence to be transcribed and a promoter.
  • the expression cassette as described herein comprises polynucleotide sequences that encode antigen-binding constructs as described herein or fragments thereof.
  • vector or "expression vector” is synonymous with "expression construct” and refers to a nucleic acid molecule that is used to introduce and direct the expression of a specific gene to which it is operably associated in a target cell.
  • the term includes the vector as a self-replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which it has been introduced.
  • the expression vector as described herein comprises an expression cassette. Expression vectors allow transcription of large amounts of stable mRNA. Once the expression vector is inside the target cell, the ribonucleic acid molecule or protein that is encoded by the gene is produced by the cellular transcription and/or translation machinery.
  • the expression vector as described herein comprises an expression cassette that comprises polynucleotide sequences that encode antigen-binding constructs as described herein or fragments thereof. Exemplary vectors are described herein.
  • a host cell is transformed with an expression vector coding for an antigen-binding construct.
  • Cell "host cell”, “cell line” and “cell culture” are used interchangeably herein and all such terms should be understood to include progeny resulting from growth or culturing of a cell.
  • Transformation and “transfection” are used interchangeably to refer to the process of introducing DNA into a cell. .
  • Host cells include “transformants” and “transformed cells,” which include the primary transformed cell and progeny derived therefrom without regard to the number of passages.
  • progeny are not completely identical in nucleic acid content to a parent cell, but may contain mutations. Mutant progeny that have the same function or biological activity as screened or selected for in the originally transformed cell are included herein.
  • a host cell is any type of cellular system that can be used to generate the antigen-binding constructs as described herein.
  • Host cells include cultured cells, e.g.
  • mammalian cultured cells such as CHO cells, BHK cells, NS0 cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells or hybridoma cells, bacteria (for example E. coli and Bacillus subtilis), yeasts (for example Saccharomyces cerevisiae, Kluyveromyces lactis and Pichia pastoris, filamentous fungi (for example Aspergillus), insect cells, and plant cells, to name only a few, but also cells comprised within a transgenic animal, transgenic plant or cultured plant or animal tissue. Additional examples of host cells are described herein.
  • the antigen-binding construct is produced in a mammalian cell.
  • the mammalian cell is selected from the group consisting of a VERO, HeLa, HEK, NS0, Chinese Hamster Ovary (CHO), W138, BHK, COS-7, Caco-2 and MDCK cell, and subclasses and variants thereof.
  • vectors containing polynucleotides encoding an antigen- binding construct described herein, host cells, and the production of the antigen-binding construct proteins by synthetic and recombinant techniques may be, for example, a phage, plasmid, viral, or retroviral vector. Retroviral vectors may be replication competent or replication defective. In the latter case, viral propagation generally will occur only in complementing host cells.
  • the polynucleotides encoding antigen-binding construct proteins described herein are joined to a vector containing a selectable marker for propagation in a host.
  • a plasmid vector is introduced in a precipitate, such as a calcium phosphate precipitate, or in a complex with a charged lipid. If the vector is a virus, it may be packaged in vitro using an appropriate packaging cell line and then transduced into host cells.
  • the polynucleotide insert is operatively linked to an appropriate promoter, such as the phage lambda PL promoter, the E. coli lac, trp, phoA and rac promoters, the SV40 early and late promoters and promoters of retroviral LTRs, to name a few.
  • an appropriate promoter such as the phage lambda PL promoter, the E. coli lac, trp, phoA and rac promoters, the SV40 early and late promoters and promoters of retroviral LTRs, to name a few.
  • Other suitable promoters will be known to the skilled artisan.
  • the expression constructs will further contain sites for transcription initiation, termination, and, in the transcribed region, a ribosome binding site for translation.
  • the coding portion of the transcripts expressed by the constructs will preferably include a translation initiating codon at the beginning and a termination codon (UAA, UGA or UAG) appropriately
  • the expression vectors will preferably include at least one selectable marker.
  • markers include dihydrofolate reductase, G418, glutamine synthase, or neomycin resistance for eukaryotic cell culture, and tetracycline, kanamycin or ampicillin resistance genes for culturing in E. coli and other bacteria.
  • Representative examples of appropriate hosts include, but are not limited to, bacterial cells, such as E. coli, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells (e.g., Saccharomyces cerevisiae or Pichia pastoris (ATCC Accession No.
  • insect cells such as Drosophila S2 and Spodoptera Sf9 cells
  • animal cells such as CHO, COS, NSO, 293, and Bowes melanoma cells
  • plant cells Appropriate culture mediums and conditions for the above-described host cells are known in the art.
  • vectors preferred for use in bacteria include pQE70, pQE60 and pQE-9, available from QIAGEN, Inc.; pBluescript vectors, Phagescript vectors, pNH8A, pNH16a, pNH18A; pNH46A, available from Stratagene Cloning Systems, Inc.; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 available from Pharmacia Biotech, Inc.
  • eukaryotic vectors are pWLNEO, pSV2CAT, pOG44, pXTl and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL available from Pharmacia.
  • Preferred expression vectors for use in yeast systems include, but are not limited to pYES2, pYDl, pTEFl/Zeo, pYES2/GS, pPICZ, pGAPZ, pGAPZalph, pPIC9, pPIC3.5, pHIL-D2, pHIL-Sl, pPIC3.5K, pPIC9K, and PA0815 (all available from Invitrogen, Carlsbad, CA).
  • polynucleotides encoding an antigen-binding construct described herein are fused to signal sequences that will direct the localization of a protein as described herein to particular compartments of a prokaryotic or eukaryotic cell and/or direct the secretion of a protein as described herein from a prokaryotic or eukaryotic cell.
  • signal sequences that will direct the localization of a protein as described herein to particular compartments of a prokaryotic or eukaryotic cell and/or direct the secretion of a protein as described herein from a prokaryotic or eukaryotic cell.
  • E. coli one may wish to direct the expression of the protein to the periplasmic space.
  • signal sequences or proteins (or fragments thereof) to which the antigen-binding construct proteins are fused in order to direct the expression of the polypeptide to the periplasmic space of bacteria include, but are not limited to, the pelB signal sequence, the maltose binding protein (MBP) signal sequence, MBP, the ompA signal sequence, the signal sequence of the periplasmic E. coli heat-labile enterotoxin B- subunit, and the signal sequence of alkaline phosphatase.
  • MBP maltose binding protein
  • ompA signal sequence the signal sequence of the periplasmic E. coli heat-labile enterotoxin B- subunit
  • alkaline phosphatase Several vectors are commercially available for the construction of fusion proteins which will direct the localization of a protein, such as the pMAL series of vectors (particularly the pMAL-.rho. series) available from New England Biolabs.
  • polynucleotides encoding proteins as described herein may be fused to the pelB pectate lyase signal sequence to increase the efficiency of expression and purification of such polypeptides in Gram-negative bacteria. See, U.S. Pat. Nos. 5,576, 195 and 5,846,818, the contents of which are herein incorporated by reference in their entireties.
  • Examples of signal peptides that are fused to an antigen-binding construct protein in order to direct its secretion in mammalian cells include, but are not limited to, the MPIF-1 signal sequence (e.g., amino acids 1-21 of GenBank Accession number AAB51134), the stanniocalcin signal sequence (MLQNSAVLLLLVISASA (SEQ ID NO: 51)), and a consensus signal sequence (MPTWAWWLFLVLLLALWAPARG(SEQ ID NO: 52)).
  • a suitable signal sequence that may be used in conjunction with baculoviral expression systems is the gp67 signal sequence (e.g., amino acids 1-19 of GenBank Accession Number AAA72759).
  • the signal sequence is an IgK secretory signal comprising the amino acid sequence (M G D N D I H F A F L S T G V H S Q V Q (SEQ ID NO: 53)).
  • the IgK secretory signal is fused to the N- terminal of an TDP-43- binding polypeptide.
  • Vectors which use glutamine synthase (GS) or DHFR as the selectable markers can be amplified in the presence of the drugs methionine sulphoximine or methotrexate, respectively.
  • An advantage of glutamine synthase based vectors are the availability of cell lines (e.g., the murine myeloma cell line, NSO) which are glutamine synthase negative.
  • Glutamine synthase expression systems can also function in glutamine synthase expressing cells (e.g., Chinese Hamster Ovary (CHO) cells) by providing additional inhibitor to prevent the functioning of the endogenous gene.
  • glutamine synthase expression system and components thereof are detailed in PCT publications: WO87/04462; WO86/05807; WO89/10036; WO89/10404; and WO91/06657, which are hereby incorporated in their entireties by reference herein. Additionally, glutamine synthase expression vectors can be obtained from Lonza Biologies, Inc. (Portsmouth, N.H.). Expression and production of monoclonal antibodies or antigen-binding constructs using a GS expression system in murine myeloma cells is described in Bebbington et al., Bio/technology 10: 169(1992) and in Biblia and Robinson Biotechnol. Prog. 11 : 1(1995) which are herein incorporated by reference.
  • host cells containing vector constructs described herein and additionally host cells containing nucleotide sequences that are operably associated with one or more heterologous control regions (e.g., promoter and/or enhancer) using techniques known of in the art.
  • the host cell can be a higher eukaryotic cell, such as a mammalian cell (e.g., a human derived cell), or a lower eukaryotic cell, such as a yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial cell.
  • a host strain may be chosen which modulates the expression of the inserted gene sequences, or modifies and processes the gene product in the specific fashion desired.
  • Expression from certain promoters can be elevated in the presence of certain inducers; thus expression of the genetically engineered polypeptide may be controlled.
  • different host cells have characteristics and specific mechanisms for the translational and post-translational processing and modification (e.g., phosphorylation, cleavage) of proteins. Appropriate cell lines can be chosen to ensure the desired modifications and processing of the foreign protein expressed.
  • Mammalian cell lines available as hosts for expression are well known in the art and include many immortalized cell lines available from the American Type Culture Collection (ATCC), including but not limited to Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (e.g., Hep G2), human epithelial kidney 293 cells, and a number of other cell lines. Cell lines of particular preference are selected through determining which cell lines have high expression levels and produce antibodies with constitutive ManLAM binding properties.
  • ATCC American Type Culture Collection
  • nucleic acids and nucleic acid constructs as described herein into the host cell can be effected by calcium phosphate transfection; DEAE-dextran mediated transfection, cationic lipid-mediated transfection, electroporation, transduction, infection, or other methods. Such methods are described in many standard laboratory manuals, such as Davis et al., Basic Methods In Molecular Biology (1986). It is specifically contemplated that the polypeptides as described herein may in fact be expressed by a host cell lacking a recombinant vector.
  • one embodiment also encompasses primary, secondary, and immortalized host cells of vertebrate origin, particularly mammalian origin, that have been engineered to delete or replace endogenous genetic material (e.g., the coding sequence corresponding to a Cargo polypeptide is replaced with an antigen-binding construct protein corresponding to the Cargo polypeptide), and/or to include genetic material.
  • endogenous genetic material e.g., the coding sequence corresponding to a Cargo polypeptide is replaced with an antigen-binding construct protein corresponding to the Cargo polypeptide
  • the genetic material operably associated with the endogenous polynucleotide may activate, alter, and/or amplify endogenous polynucleotides.
  • heterologous polynucleotides e.g., polynucleotides encoding a protein, or a fragment or variant thereof
  • heterologous control regions e.g., promoter and/or enhancer
  • endogenous polynucleotide sequences encoding a therapeutic protein via homologous recombination
  • heterologous polynucleotides e.g., polynucleotides encoding a protein, or a fragment or variant thereof
  • heterologous control regions e.g., promoter and/or enhancer
  • Antigen-binding construct proteins described herein can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography such as with protein A, hydroxyl apatite chromatography, hydrophobic charge interaction chromatography and lectin chromatography. Most preferably, high performance liquid chromatography (“HPLC”) is employed for purification.
  • HPLC high performance liquid chromatography
  • the antigen-binding construct proteins as described herein are purified using Anion Exchange Chromatography including, but not limited to, chromatography on Q-sepharose, DEAE sepharose, poros HQ, poros DEAF, Toyopearl Q, Toyopearl QAE, Toyopearl DEAE, Resource/Source Q and DEAE, Fractogel Q and DEAE columns.
  • Anion Exchange Chromatography including, but not limited to, chromatography on Q-sepharose, DEAE sepharose, poros HQ, poros DEAF, Toyopearl Q, Toyopearl QAE, Toyopearl DEAE, Resource/Source Q and DEAE, Fractogel Q and DEAE columns.
  • proteins described herein may be purified using
  • Cation Exchange Chromatography including, but not limited to, SP-sepharose, CM sepharose, poros HS, poros CM, Toyopearl SP, Toyopearl CM, Resource/Source S and CM, Fractogel S and CM columns and their equivalents and comparables.
  • antigen-binding construct proteins described herein can be chemically synthesized using techniques known in the art (e.g., see Creighton, 1983, Proteins: Structures and Molecular Principles, W. H. Freeman & Co., N.Y and Hunkapiller et al., Nature, 310: 105-111 (1984)).
  • a polypeptide corresponding to a fragment of a polypeptide can be synthesized by use of a peptide synthesizer.
  • nonclassical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the polypeptide sequence.
  • Non-classical amino acids include, but are not limited to, to the D-isomers of the common amino acids, 2,4diaminobutyric acid, alpha-amino isobutyric acid, 4aminobutyric acid, Abu, 2-amino butyric acid, g-Abu, e-Ahx, 6amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, ⁇ -alanine, fluoro-amino acids, designer amino acids such as ⁇ -methyl amino acids, Coc-methyl amino acids, Na-methyl amino acids, and amino acid analogs in general.
  • the amino acid can be D (dextrorotary) or L (levorotary).
  • cell-free protein expression systems are utilized to co- express polypeptides (e.g., heavy and light chain polypeptides) without the use of living cells. Instead, all components needed to transcribe DNA to RNA and translate the RNA to protein (e.g. ribosomes, tRNAs, enzymes, cofactors, amino acids) are provided in solution for use in vitro.
  • the in vitro expression requires (1) the genetic template (mRNA or DNA) encoding the heavy and light chain polypeptides and (2) a reaction solution containing the necessary transcriptional and translational molecular machinery.
  • cell extracts substantially supply components of the reaction solution, for instance: RNA polymerases for mRNA transcription, ribosomes for polypeptide translation, tRNA, amino acids, enzymatic cofactors, an energy source, and cellular components essential for proper protein folding.
  • Cell-free protein expression systems can be prepared using lysates derived from bacterial cells, yeast cells, insect cells, plant cells, mammalian cells, human cells or combinations thereof. Such cell lysates can provide the correct composition and proportion of enzymes and building blocks required for translation.
  • cell membranes are removed to leave only the cytosolic and organelle components of the cell.
  • cell-free protein expression systems are known in the art as reviewed in Carlson et al. (2012) Biotechnol. Adv. 30: 1185-1194.
  • cell-free protein expression systems are available based on prokaryotic or eukaryotic cells.
  • prokaryotic cell-free expression systems include those from E. coli.
  • Eukaryotic cell-free protein expression systems are available based on extracts from rabbit reticulocytes, wheat germ, and insect cells, for example.
  • prokaryotic and eukaryotic cell-free protein expression systems are commercially available from companies such as Roche, Invitrogen, Qiagen, and Novagen.
  • cell-free protein expression systems that would produce polypeptides (e.g., heavy chain and light chain polypeptides) that are capable of pairing with each other.
  • the cell-free protein expression system can also be supplemented with chaperones (e.g. BiP) and isomerases (e.g. disulphide isomerase) to improve the efficiency of IgG folding.
  • chaperones e.g. BiP
  • isomerases e.g. disulphide isomerase
  • cell-free expression systems are utilized to co- express the heavy and light chain polypeptides from DNA templates (transcription and translation) or mRNA templates (translation only).
  • the antigen-binding construct is produced in a yeast cell.
  • the yeasts are transformed with a coding sequence for the desired protein in any of the usual ways, for example electroporation. Methods for transformation of yeast by electroporation are disclosed in Becker & Guarente (1990) Methods Enzymol. 194, 182.
  • Useful yeast plasmid vectors include pRS403-406 and pRS413-416 and are generally available from Stratagene Cloning Systems, La Jolla, Calif. 92037, USA.
  • Plasmids pRS403, pRS404, pRS405 and pRS406 are Yeast Integrating plasmids (Yips) and incorporate the yeast selectable markers HIS3, 7RP1, LEU2 and URA3.
  • Plasmids pRS413- 416 are Yeast Centromere plasmids (Ycps).
  • Exemplary genera of yeast contemplated to be useful in one embodimentas hosts for expressing the proteins are Pichua (formerly classified as Hansenula), Saccharomyces, Kluyveromyces, Aspergillus, Candida, Torulopsis, Torulaspora, Schizosaccharomyces, Citeromyces, Pachysolen, Zygosaccharomyces, Debaromyces, Trichoderma, Cephalosporium, Humicola, Mucor, Neurospora, Yarrowia, Metschunikowia, Rhodosporidium, Leucosporidium, Botryoascus, Sporidiobolus, Endomycopsis, and the like.
  • Saccharomyces spp. are S. cerevisiae, S. italicus and S. rouxii.
  • Kluyveromyces spp. are K. fragilis, K. lactis and K. marxianus.
  • Torulaspora species is T. delbrueckii.
  • Examples of Pichia (Hansenula) spp. are P. angusta (formerly H. polymorpha), P. anomala (formerly H. anomala) and P. pastoris.
  • Methods for the transformation of S. cerevisiae are taught generally in EP 251 744, EP 258 067 and WO 90/01063, all of which are incorporated herein by reference.
  • Exemplary species of Saccharomyces useful for the synthesis of antigen- binding constructs described herein include S. cerevisiae, S. italicus, S. diastaticus, and Zygosaccharomyces rouxii.
  • Preferred exemplary species of Kluyveromyces include K. fragilis and K. lactis.
  • Preferred exemplary species of Hansenula include H. polymorpha (now Pichia angusta), H. anomala (now Pichia anomala), and Pichia capsulata. Additional preferred exemplary species of Pichia include P. pastoris.
  • Preferred exemplary species of Aspergillusin include A. niger and A. nidulans.
  • Preferred exemplary species of Yarrowia include Y. lipolytica.
  • Many preferred yeast species are available from the ATCC.
  • the following preferred yeast species are available from the ATCC and are useful in the expression of proteins: Saccharomyces cerevisiae, Hansen, teleomorph strain BY4743 yap3 mutant (ATCC Accession No. 4022731); Saccharomyces cerevisiae Hansen, teleomorph strain BY4743 hspl50 mutant (ATCC Accession No. 4021266); Saccharomyces cerevisiae Hansen, teleomorph strain BY4743 pmtl mutant (ATCC Accession No.
  • Saccharomyces cerevisiae Hansen, teleomorph ATCC Accession Nos. 20626; 44773; 44774; and 62995
  • Saccharomyces diastaticus Andrews et Gilliland ex van der Walt, teleomorph ATCC Accession No. 62987
  • Kluyveromyces lactis Dombrowski
  • van der Walt teleomorph
  • Pichia angusta Teunisson et al.
  • Kurtzman teleomorph deposited as Hansenula polymorpha de Morais et Maia, teleomorph (ATCC Accession No.
  • Suitable promoters for S. cerevisiae include those associated with the PGKI gene, GAL1 or GALIO genes, CYCI, PH05, TRP1, ADH1, ADH2, the genes for glyceraldehyde-3 -phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, triose phosphate isomerase, phosphoglucose isomerase, glucokinase, alpha-mating factor pheromone, [a mating factor pheromone], the PRBI promoter, the GUT2 promoter, the GPDI promoter, and hybrid promoters involving hybrids of parts of 5' regulatory regions with parts of 5' regulatory regions of other promoters or with upstream activation sites (e.g. the promoter of EP-A-258 067).
  • Convenient regulatable promoters for use in Schizosaccharomyces pombe are the thiamine-repressible promoter from the nmt gene as described by Maundrell (1990) J. Biol. Chem. 265, 10857-10864 and the glucose repressible jbpl gene promoter as described by Hoffman & Winston (1990) Genetics 124, 807-816. [00149] Methods of transforming Pichia for expression of foreign genes are taught in, for example, Cregg et al. (1993), and various Phillips patents (e.g. U.S. Pat. No.
  • Suitable promoters include AOX1 and AOX2.
  • Gleeson et al. (1986) J. Gen. Microbiol. 132, 3459-3465 include information on Hansenula vectors and transformation, suitable promoters being MOX1 and FMD1; whilst EP 361 991, Fleer et al. (1991) and other publications from Rhone-Poulenc Rorer teach how to express foreign proteins in Kluyveromyces spp., a suitable promoter being PGKI.
  • the transcription termination signal is preferably the 3' flanking sequence of a eukaryotic gene which contains proper signals for transcription termination and polyadenylation.
  • Suitable 3' flanking sequences may, for example, be those of the gene naturally linked to the expression control sequence used, i.e. may correspond to the promoter. Alternatively, they may be different in which case the termination signal of the S. cerevisiae ADHI gene is preferred.
  • the desired antigen-binding construct protein is initially expressed with a secretion leader sequence, which may be any leader effective in the yeast chosen.
  • leader sequence useful in S. cerevisiae include that from the mating factor alpha polypeptide (MFoc-1) and the hybrid leaders of EP-A-387 319. Such leaders (or signals) are cleaved by the yeast before the mature protein is released into the surrounding medium. Further such leaders include those of S.
  • SUC2 cerevisiae invertase disclosed in JP 62- 096086 (granted as 911036516), acid phosphatase (PH05), the pre-sequence of MFoc-1, 0 glucanase (BGL2) and killer toxin; S. diastaticus glucoarnylase II; S. carlsbergensis oc- galactosidase (MEL1); K. lactis killer toxin; and Candida glucoarnylase.
  • S. diastaticus glucoarnylase II S. carlsbergensis oc- galactosidase (MEL1)
  • K. lactis killer toxin and Candida glucoarnylase.
  • antigen-binding constructs described herein which are differentially modified during or after translation.
  • the modification is at least one of: glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage and linkage to an antibody molecule or antigen-binding construct or other cellular ligand.
  • the antigen-binding construct is chemically modified by known techniques, including but not limited, to specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBH 4 ; acetylation, formylation, oxidation, reduction; and metabolic synthesis in the presence of tunicamycin.
  • Additional post-translational modifications of antigen-binding constructs described herein include, for example, N-linked or O-linked carbohydrate chains, processing of N-terminal or C-terminal ends), attachment of chemical moieties to the amino acid backbone, chemical modifications of N-linked or O-linked carbohydrate chains, and addition or deletion of an N-terminal methionine residue as a result of procaryotic host cell expression.
  • the antigen-binding constructs described herein are modified with a detectable label, such as an enzymatic, fluorescent, isotopic or affinity label to allow for detection and isolation of the protein.
  • examples of suitable enzyme labels include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase;
  • examples of suitable prosthetic group complexes include streptavidin biotin and avidin/biotin;
  • examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol;
  • examples of bioluminescent materials include luciferase, luciferin, and aequorin;
  • examples of suitable radioactive material include iodine, carbon, sulfur, tritium, indium, technetium, thallium, gallium, palladium, molybdenum, xenon, fluorine.
  • the antigen-binding constructs described herein are modified by either natural processes, such as post-translational processing, or by chemical modification techniques which are well known in the art.
  • the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide.
  • polypeptides from antigen-binding constructs described herein are branched, for example, as a result of ubiquitination, and in some embodiments are cyclic, with or without branching. Cyclic, branched, and branched cyclic polypeptides are a result from posttranslation natural processes or made by synthetic methods.
  • Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination.
  • antigen-binding constructs described herein are attached to solid supports, which are particularly useful for immunoassays or purification of polypeptides that are bound by, that bind to, or associate with proteins as described herein.
  • solid supports include, but are not limited to, glass, cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride or polypropylene.
  • a method of treating a disease or disorder characterized by TDP-43 proteinopathy comprising administering to a subject in which such treatment, prevention or amelioration is desired, an TDP-43 antigen-binding construct described herein, in an amount effective to treat, prevent or ameliorate the disease or disorder.
  • disorders or “disease” refers to any condition that would benefit from treatment with an anti-TDP-43 antibody or method as described herein. This includes chronic and acute disorders or diseases including those pathological conditions which predispose the mammal to the disorder in question.
  • the diseases being treated with the antigen-binding constructs described herein are associated with TDP proteinopathy.
  • ALS amyotophic lateral sclerosis
  • Parkinson's disease frontotemporal lobar degeneration (FTLD) motor neuron disease
  • Alzheimer's disease dementia with Lewy bodies
  • Huntington's disease Lewy body disease
  • MCI mild cognitive impairment
  • TDP-43 abnormalities triggered by nerve injury brain trauma, brain ischemia (stroke).
  • the term "subject" refers to an animal, in some embodiments a mammal, which is the object of treatment, observation or experiment.
  • An animal may be a human, a non-human primate, a companion animal (e.g., dogs, cats, and the like), farm animal (e.g., cows, sheep, pigs, horses, and the like) or a laboratory animal (e.g., rats, mice, guinea pigs, and the like).
  • mammal as used herein includes but is not limited to humans, non-human primates, canines, felines, murines, bovines, equines, and porcines.
  • the subject being treated with the anti-TDP-43 antigen-binding constructs is a mouse or a human.
  • Treatment refers to clinical intervention in an attempt to alter the natural course of the individual or cell being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include preventing occurrence or recurrence of disease, alleviation of symptoms, diminishing of any direct or indirect pathological consequences of the disease, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis.
  • antigen-binding constructs as described herein are used to delay development of a disease or disorder.
  • Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis.
  • constructs described herein are used to delay development of a disease or to slow the progression of a disease.
  • the term "effective amount” as used herein refers to that amount of construct being administered, which will accomplish the goal of the recited method, e.g., relieve to some extent one or more of the symptoms of the disease, condition or disorder being treated.
  • the amount of the composition described herein which will be effective in the treatment, inhibition and prevention of a disease or disorder associated with aberrant expression and/or activity of a therapeutic protein can be determined by standard clinical techniques.
  • in vitro assays may optionally be employed to help identify optimal dosage ranges.
  • the precise dose to be employed in the formulation will also depend on the route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. Effective doses are extrapolated from dose-response curves derived from in vitro or animal model test systems.
  • TDP-43 antigen-binding constructs described herein are administered to the subject.
  • Various delivery systems are known and can be used to administer an antigen- binding construct formulation described herein, e.g., encapsulation in liposomes, microparticles, microcapsules, recombinant cells capable of expressing the compound, receptor-mediated endocytosis (see, e.g., Wu and Wu, J. Biol. Chem. 262:4429-4432 (1987)), construction of a nucleic acid as part of a retroviral or other vector, etc.
  • Methods of introduction include but are not limited to intradermal, intramuscular, intraperitoneal, intrathecal, intravenous, subcutaneous, intranasal, epidural, and oral routes.
  • the compounds or compositions may be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, etc.) and may be administered together with other biologically active agents. Administration can be systemic or local.
  • intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir, such as an Ommaya reservoir.
  • Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent.
  • the antigen-binding constructs, or compositions described herein may be administered locally to the area in need of treatment; this may be achieved by, for example, and not by way of limitation, local infusion during surgery, topical application, e.g., in conjunction with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers.
  • care must be taken to use materials to which the protein does not absorb.
  • the antigen-binding constructs or composition can be delivered in a vesicle, in particular a liposome (see Langer, Science 249: 1527-1533 (1990); Treat et al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez- Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid).
  • a liposome see Langer, Science 249: 1527-1533 (1990); Treat et al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez- Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid).
  • the antigen-binding constructs or composition can be delivered in a controlled release system.
  • a pump may be used (see Langer, supra; Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987); Buchwald et al., Surgery 88:507 (1980); Saudek et al., N. Engl. J. Med. 321 :574 (1989)).
  • polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Fla.
  • a controlled release system can be placed in proximity of the therapeutic target, e.g., the brain, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, in Medical Applications of Controlled Release, vol. 2, pp. 115-138 (1984)).
  • nucleic acid encoding antigen-binding constructs described herein can be administered in vivo to promote expression of its encoded protein, by constructing it as part of an appropriate nucleic acid expression vector and administering it so that it becomes intracellular, e.g., by use of a retroviral vector (see U.S. Pat. No.
  • a nucleic acid can be introduced intracellularly and incorporated within host cell DNA for expression, by homologous recombination.
  • the nucleic acid encoding the antigen-binding construct is inserted into an adeno-associated virus (AAV) vector (see Patel et al., Molecular Therapy 22 (3) 498-510 (2014) and Example 12 herein).
  • AAV adeno-associated virus
  • the viral vector may be administered to the subject systemically or locally, for example by intrathecal injection.
  • an antigen-binding construct described herein is administered as a combination with antigen-binding constructs with non-overlapping binding target epitopes on TDP-43.
  • the amount of the antigen-binding construct which will be effective in the treatment, inhibition and prevention of a disease or disorder can be determined by standard clinical techniques.
  • in vitro assays may optionally be employed to help identify optimal dosage ranges.
  • the precise dose to be employed in the formulation will also depend on the route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. Effective doses are extrapolated from dose-response curves derived from in vitro or animal model test systems.
  • a method of preventing or delaying the onset of at least one symptom of a TDP-43 proteinopathy in a subject in need thereof comprising administering a therapeutically effective amount of an TDP-43 antigen binding construct described herein.
  • the subject is an experimental organism, such as, but not limited to, a transgenic mouse.
  • the subject is a human.
  • antigen-binding constructs described herein may be administered alone or in combination with other types of treatments used for neurodegenerative diseases, such as Rilutek ® .
  • TDP-43 antigen-binding constructs described herein can be characterized using any in vivo or in vitro models of TDP-43 proteinopathies.
  • a person skilled in the art understands that an TDP-43 antigen-binding construct can be characterized in a mouse model for TDP-43 proteinopathies, for example, one of the animal models for TDP-43 proteinopathies described in Swamp et al. Brain 134: 2610-2626 (2011).
  • Swarup et al. 2011 describes three transgenic mouse models for TDP proteinopathies: wild type, G348C and A315T. These transgenic mice exhibit motor and cognitive impairment (as measured by the Barnes maze test, the step through passive avoidance test and the accelerating rotarod test).
  • mice exhibit cytoplasmic TDP-43 -positive ubiquitinated inclusions, intermediate filament abnormalities, axonopathy and neuroinflammation.
  • Additional animal models are described in Wegorzewska et al, Proc. Natl. Acad. Sci. U.S.A. 106 (2009), 18809-14; Gurney et al, Science 264 (1994), 1 772-75; Shan et al, Neuropharmacol. Letters 458 (2009), 70-74; Wils et al, Proc. Natl. Acad. Sci. USA. 106 (2010), 3858-63; Duchen and Strich, J. Neurol.
  • An experimental model of TDP-43 proteinopathy can be used in a preventative setting or it can be used in a therapeutic setting.
  • a preventative setting the dosing of animals starts prior to the onset of the TDP-43 proteinopaihy or symptoms thereof.
  • An TDP-43 antigen-binding construct described herein may be evaluated for its ability to prevent, reduce or delay the onset of TDP- 43 proteinopaihy or symptoms thereof.
  • a therapeutic model the dosing of animals starts after the onset of TDP-43 proteinopaihy or a symptom thereof.
  • an TDP-43 antigen-binding constructs is evaluated for its ability to treat, reduce or alleviate the TDP-43 proteinopaihy or a symptom thereof.
  • TDP-43 proteinopathies include, but are not limited to, accumulation of pathological TDP-43 deposits, pathological TDP-43 distribution, phosphorylated TDP-43, or insoluble TDP-43 fractions in the neurons, brain, spinal cord, cerebrospinal fluid or serum of the experimental object.
  • a positive preventative or therapeutic outcome in any animal model of TDP-43 proteinopathies indicates that the particular TDP-43 antigen-binding construct can be used for preventative or therapeutic purposes in a subject other than the experimental model organism, for example, it can be used to treat TDP-43 proteinopathies in a human subject in need thereof.
  • an TDP-43 antigen-binding construct can be administered to a TDP-43 proteinopathy mouse model and corresponding control wild type mice.
  • the antigen-binding construct administered can be a murine antibody, or a human- murine chimera.
  • the TDP-43 antigen-binding constructs can be administered by any means known in the art, for example, by intraperitoneal, intracranial, intramuscular, intrathecal, intravenous, subcutaneous, oral, and aerosol administration. Experimental animals can be given one, two, three, four, five or more doses of the TDP-43 antigen-binding constructs or a control composition, such as PBS.
  • experimental animals will be administered one or two doses of an TDP-43 antigen-binding construct.
  • the animals are chronically dosed with the TDP-43 antigen-binding constructs over several weeks or months.
  • a skilled, artisan can readily design a dosing regimen that fits the experimental purpose, for example, dosing regimen for acute studies, dosing regimen for chronic studies, dosing regimen for toxicity studies, dosing regimen for preventative or therapeutic studies.
  • the presence of the TDP-43 antigen-binding constructs in a particular tissue compartment of the experimental animals for example, but not limited to, serum, blood, cerebrospinal fluid, brain or spinal cord tissue, can be established using well know methods of the art.
  • a TDP-43 antigen-binding construct is capable of penetrating the blood brain barrier. In another embodiment, a TDP-43 antigen- binding constructs is capable of entering neurons. By adjusting the dose of the TDP-43 antigen-binding construct and the dosing frequency, a desired concentration can be maintained in the experimental animals. Any effect of a TDP-43 antigen-binding construct as described herein in the TDP-43 proteinopathy models can be assessed by comparing the level, biochemical characteristics or distribution of TDP-43 in the treated and control animals. In one embodiment, a TDP-43 antigen-binding construct is capable of reducing the level, amount or concentration of TDP-43 inclusions in the brain or spinal cord in an animal model.
  • the construct can reduce the level, amount or concentration of TDP-43 inclusions by at least about 5%, 10%, 20%, 30%, 50%, 70%, 90% or more.
  • a TDP-43 antigen-binding construct is capable of reducing the number or frequency of TDP-43 inclusion-positive neurons in the brain or spinal cord in an animal model, for example, by at least about 5%, 10%, 20%, 30%, 50%o, 70%, 90% or more.
  • the effect of a TDP-43 antigen-binding construct can also be assessed by examining the distribution and biochemical properties of TDP-43 following administration.
  • a TDP-43 antigen-binding construct is capable of reducing the amount or concentration of cytoplasmic or nuclear TDP-43 protein in the brain or spinal cord of an animal model, for example, by at least about 5%, 10%, 20%, 30%, 50%, 70%, 90% or more, in another embodiment, it is capable of reducing the amount or concentration of neuritic TDP-43 protein in the brain or spinal cord of an animal model, for example, by at least about 5%, 10%, 20%, 30%, 50%, 70%. 90% or more, in a further embodiment, it can reduce the amount or concentration of phosphorylated TDP-43 protein in the brain or spinal cord in an animal model, for example, by at least about 5%, 10%, 20%, 30%, 50%, 70%), 90% or more.
  • TDP-43 antigen-binding construct can also alter, for example, reduce or increase TDP-43 concentration in the blood, serum or cerebrospinal fluid of an animal model, for example, by at least about 5%, 10%, 20%, 30%, 50%), 70%), 90%) or more, in one embodiment, the % reduction or increase is relative compared to the level, number, frequency, amount or concentration that existed before treatment, or to the level, number, frequency, amount or concentration that, exist in an untreated/control treated subject.
  • a TDP-43 antigen-binding construct can prevent or delay the onset of at least one symptom of a TDP-43 proteinopathy in a subject. In one embodiment, a TDP-43 antigen-binding construct can reduce or eliminate at least one symptom of a TDP-43 proteinopathy in a subject.
  • the symptom can be the formation of pathological TDP-43 deposits, phosphorylated TDP-43 deposits, or insoluble TDP-43 deposits.
  • the symptom can also be the presence, or elevated concentration or amount, of TDP-43 in the serum, blood, urine or cerebrospinal fluid, wherein elevated concentration amount is compared to a healthy subject.
  • the symptom is the presence of TDP-43 -associated NF-kB.
  • the symptom can be a neurological symptom., for example, loss of motor function or cognitive impairment.
  • memory impairment is assessed using the Barnes maze test or the step through passive avoidance test.
  • motor function impairment is assessed using the accelerating rotarod test.
  • at least one symptom is reduced by at least about 5%, 10%, 15%, 20%, 30%, 50%, 70%, or 90%.
  • the latency time on the rotarod apparatus is significantly higher in a treated subject than in a control subject.
  • the rotarod latency time is increased by at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%. Kits and articles of manufacture
  • kits comprising one or more anti-TDP-43 antigen binding constructs.
  • Individual components of the kit would be packaged in separate containers and, associated with such containers, can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale.
  • the kit may optionally contain instructions or directions outlining the method of use or administration regimen for the antigen binding construct.
  • the container means may itself be an inhalant, syringe, pipette, eye dropper, or other such like apparatus, from which the solution may be administered to a subject or applied to and mixed with the other components of the kit.
  • the components of the kit may also be provided in dried or lyophilized form and the kit can additionally contain a suitable solvent for reconstitution of the lyophilized components.
  • the kits described herein also may comprise an instrument for assisting with the administration of the composition to a patient.
  • Such an instrument may be an inhalant, nasal spray device, syringe, pipette, forceps, measured spoon, eye dropper or similar medically approved delivery vehicle.
  • an article of manufacture containing materials useful for the treatment, prevention and/or diagnosis of the disorders described above comprises a container and a label or package insert on or associated with the container.
  • Suitable containers include, for example, bottles, vials, syringes, IV solution bags, etc.
  • the containers may be formed from a variety of materials such as glass or plastic.
  • the container holds a composition which is by itself or combined with another composition effective for treating, preventing and/or diagnosing the condition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).
  • At least one active agent in the composition is a T cell activating antigen binding construct described herein.
  • the label or package insert indicates that the composition is used for treating the condition of choice.
  • the article of manufacture may comprise (a) a first container with a composition contained therein, wherein the composition comprises an antigen-binding construct described herein; and (b) a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent.
  • the article of manufacture in this embodiment described herein may further comprise a package insert indicating that the compositions can be used to treat a particular condition.
  • the article of manufacture may further comprise a second (or third) container comprising a pharmaceutically-acceptable buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes.
  • TDP-43 antigen-binding constructs may be used in the diagnosis of TDP-43 proteinopathies, particularly amyotrophic lateral sclerosis and/or frontotemporal lobar degeneration.
  • TDP-43 antigen-binding constructs may be used in the diagnosis and/or monitoring of a subject predisposed or suspected of developing a neurodegenerative disease or suffering from a neurodegenerative disease.
  • the TDP-43 antigen-binding constructs may also be used in monitoring the efficacy of a treatment administered to a subject suffering from a TDP proteinopathy.
  • Assay methods are provided in co-owned patent application published as WO 2012/174666A1 (herein incorporated by reference) for determining the level of interaction between a TDP-43 polypeptide or fragment thereof and a NF-kB p65 polypeptide or fragment thereof in a biological sample of the subject.
  • Such assay methods may employ a TDP-43 binding construct described herein.
  • An elevated level of interaction between TDP- 43 polypeptide or fragment thereof and p65 polypeptide or fragment thereof in the biological sample relative to a reference level of interaction between TDP-43 polypeptide or fragment thereof and p65 polypeptide or fragment thereof indicates that the subject is predisposed or suspected of developing a neurodegenerative disease or is suffering from a neurodegenerative disease.
  • Further methods of using the TDP-43 antigen-binding constructs described herein to detect the association of TDP-43 and NF-kB are provided in the Examples below.
  • the TDP-43 antigen-binding constructs or nucleic acids encoding them may be used in a diagnostic composition as reagents in immuno- or nucleic acid-based diagnostic methods.
  • the TDP-43 antigen-binding constructs as described herein are, for example, suited for use in immunoassays in which they can be utilized in liquid phase or bound to a solid phase carrier.
  • immunoassays which can utilize the TDP-43 antigen-binding constructs as described herein are competitive and noncompetitive immunoassays in either a direct or indirect format. Examples of such immunoassays are the radioimmunoassay ( IA), the sandwich (immunometric assay), flow cytometry and the Western blot assay.
  • the antigen-binding constructs as described herein may be labeled for use in an assay.
  • labels and methods of labeling known to those of ordinary skill in the art. Examples of the types of labels which can be used inone embodimentinclude enzymes, radioisotopes, colloidal metals, fluorescent compounds, chemiluminescent compounds, and bioluminescent compounds.
  • the TDP-43 antigen-binding constructs as described herein can also be used in a method for the diagnosis of a disorder in an individual by obtaining a sample from the tested individual which can be a blood sample, a lymph sample, cerebrospinal fluid, or a neural tissue biopsy sample and contacting the sample with a TDP-43 antigen-binding constructs under conditions enabling the formation of antibody-antigen complexes. The level of such complexes is then determined by methods known in the art. A level significantly higher than that formed in a control sample indicating the disease in the tested individual.
  • One embodiment is a method of diagnosing a TDP-43 proteinopathy in a subject, the method comprising: (a) assessing the level of TDP-43 in a sample from the subject to be diagnosed with an TDP-43 antigen-binding construct, and (b) comparing the level of TDP-43 observed to a reference standard that indicates the level of the TDP-43 in one or more control subjects, wherein a difference or similarity between the level of the TDP-43 and the reference standard indicates that the subject suffers from a TDP-43 proteinopathy.
  • the subject to be diagnosed can be asymptomatic or preclinical for the disease.
  • the control subject has a TDP-43 proteinopathy, for example ALS or FTLD, wherein a similarity between the level of TDP-43 and the reference standard indicates that the subject, to be diagnosed has a TDP-43 proteinopathy.
  • the level of TDP-43 can be assessed by any suitable method known in the art comprising, e.g., analyzing TDP-43 by one or more techniques chosen from Western blot, immunoprecipitation, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), fluorescent activated cell sorting (FACS), or gel electrophoresis.
  • ELISA enzyme-linked immunosorbent assay
  • RIA radioimmunoassay
  • FACS fluorescent activated cell sorting
  • EXAMPLE 1 Generation of exemplary monoclonal antibodies against the TDP-43 RRMl domain of TDP-43
  • a series of exemplary monoclonal antibodies against a recombinant protein encoding the RRMl domain of TDP-43 were generated.
  • the TDP-43 fragment used as antigen was generated and purified as follows.
  • the EcoRl-Notl 428 bp hTDP43 cDNA fragment encoding RRMl was PCR-amplified and cloned into the pGEX-6P-l vector (GE Healthcare).
  • This recombinant plasmid was used to transform the E.Coli host BL21 for the expression of the 136 aa protein encoding all the RRMl domain of hTDP43.
  • the 15.68 kDa recombinant protein was subsequently purified using the Glutathione S-transferase (GST) gene fusion system (GE Healthcare).
  • GST Glutathione S-transferase
  • the exemplary anti-TDP-43 monoclonal antibodies that were obtained using standard hybridoma technology yielded an immunodetection signal for TDP-43 protein when tested by immunoblotting after SDS- PAGE of spinal cord extracts from non-transgenic mice, as well as from transgenic mice over-expressing human TDP-43 (data not shown).
  • Antibodies from three hybridoma clones CIO, G8 and E6 also detected TDP-43 on immunoblots of nuclear extracts from mouse microglial BV-2 cells fractionated by SDS-PAGE (shown in Figure 1).
  • EXAMPLE 2 Human recombinant F- ⁇ p65 interacts directly with human recombinant TDP-43
  • BSA 0.8 ug/ml or human recombinant TDP-43 in serial dilutions from 0.8 ug/ml to 0.0125 ug/ml were prepared in PBS, loaded on ELISA microplates (6 wells per conditions) and incubated overnight.
  • Human recombinant p65-His-Tag (Enzo Life Sciences) was prepared at the concentration of 0.2 ug/ml, added to all wells and incubated 2h. After 2h incubation in Blocking Buffer, anti-His-Tag-HRP (1 : 10.000) (Abeam) was prepared in Diluent Solutions, loaded on the plate and incubated 2h. Substrate Solution was added and Absorbance read at 450 nm. The results are shown in Figure 2. Values are expressed as mean ⁇ sem.
  • EXAMPLE 3 Interaction between recombinant TDP-43 and F- ⁇ p65 is inhibited by exemplary bivalent monoclonal anti-RRMl -TDP-43 antibodies CIO, G8 and E6
  • Human recombinant TDP-43 was prepared at the concentration of 0.2 ug/ml, loaded on ELISA microplates and incubated overnight.
  • p65-His-Tag (0.4 ug/ml) was mixed 1 : 1 with PBS, BSA (0.4 ug/ml), anti-TDP-43 polyclonal antibodies (Proteintech) (0.4 ug/ml IgG) or anti-RRMl -TDP-43 monoclonal antibodies (CIO, G8 or E6 monoclonalshaving an Fab/Fab format with an Fc domain) (0.4 ug/ml IgG) to reach the final concentration of 0.2 ug/ml p65 and 0.2 ug/ml interfering antibody.
  • VH variable regions of heavy chain
  • Vk variable regions of heavy chain
  • VH and Vk domains were assembled and linked together to yield a full- length scFv gene.
  • the scFv gene was constructed in a VH-linker-Vk format together with a standard flexible 20-amino acid linker (Gly4Ser)3 and it was then subcloned upstream of the Myc-tagged Pswl scFVDl .3 Tagl expression vector (Patel et al. op. cit.) to generate scFv-TDP-43. Exemplary clones were then sequenced.
  • the scFv generated contained a murine immunoglobulin (Ig) ⁇ -secretory signal for efficient secretion and a human c-myc epitope to facilitate detection. A schematic drawing of these constructs is shown in Figure 4.
  • EXAMPLE 5 Anti-TDP-43 antibodies having an scFv format localize in the cytoplasm and nucleus of HEK 293 cells, and are secreted
  • Hek 293 cells were transiently transfected with pScFv9 expression plasmid containing IgK domain, Myc-tag and a combination of the two VH and VK obtained from the E6 clone, i.e. VHlVk9, VHlVkl l, VH7Vk9 and VH7Vkl l .
  • a schematic representation of the constructs is shown in Figure 4A.
  • Cells were transfected with 4 ⁇ g of plasmid for 48h and then collected. Cytoplasmic and nuclear fractions were obtained and loaded on a 12% gel. Rabbit polyclonal anti-myc antibody (Abeam) was used to detect the ScFv antibodies inside the cells.
  • EXAMPLE 6 anti-TDP-43 antibodies having an scFv format detect TDP-43 RRMl domain
  • EXAMPLE 7 E6 VHlVk9 and E6 VH7Vk9 exemplary antigen-binding constructs in an scFv format block the interaction of TDP-43 with F- ⁇ p65
  • EXAMPLE 8 Antibodies expressed in HEK293 cells interact with TDP-43 intracellularly
  • Cell lysates were made from E6_VHlVk9- and E6_VH7Vk9-expressing HEK293 cells. The lysates were exposed to polyclonal anti-TDP 43 to immunoprecipate cellular TDP-43. Immunopreciptates were resolved using PAGE. The results are shown in Figure 8, demonstrating that the scFv antibodies E6_VHlVk9 and E6_VH7Vk9 (detected by a myc tag) were co-immunoprecipitated with TDP-43. This demonstrates that the antigen-binding constructs E6_VH1VK9 and E6_VH7VK9 bound to intracellular TDP-43.
  • EXAMPLE 9 VHlVk9 antibody blocks the interaction of TDP-43 with F-KB p65 in HEK293 cells
  • EXAMPLE 10 Inhibition of F- ⁇ activation by scFv exemplary antibodies against TDP-43 in cultured cell systems
  • a cell line was previously generated by stable transfection of BV-2 microglial cells with stable insertion of a luciferase reporter 4kBwt luciferase plasmid and subsequent selection with hygomycin (Swamp, 2011 J. Exp. Med. op cit).
  • Expression plasmid vectors encoding scFv anti-TDP-43 antibodies were transfected into these BV-2 cultured cells and transiently expressed for 48 hours. During the final 4 hours, cells were exposed to either PBS (control) or 500ng/ml LPS. Cells were lysed with Glo Buffer (Promega) and 50 ⁇ of lysates were loaded in replicates on a 96 well plate.
  • Luciferase substrate was added following the assay procedures (Bright-Glo Luciferase Assay, Promega). RLU (relative light units) of luminescence were determined using an automatic plate reader and normalized on total proteins ( ⁇ g) present in the well, as determined by protein quantification (Biorad).
  • EXAMPLE 11 Expression of scFv antibodies in Neuro2A cells caused reduction in levels of nuclear TDP-43
  • Neuro 2A cells were transiently trasfected with E6_VHlVk9, E6_Vh7Vk9 or an empty vector as in Example 5. After 48 hours, nuclear extracts were obtained from the cells and the amount of nuclear TDP-43 was quantified by ponceau staining. The results are shown in Figure 11. Both E6_VHlVk9, E6_Vh7Vk9 reduced the amount of nuclear TDP-43 significantly. In ALS, there is an upregulation of TDP-43 mRNA and protein levels (Swarup et al. J Exp med 2011). This result suggests that anti-TDP-43 scFv antibodies might confer protection by attenuating the upregulation of TDP-43 in ALS.
  • EXAMPLE 12 Production of adeno-associated viral AAV vectors containing scFv antibodies [00216] The following protocol was used to produce pscAAV vectors containing E6- derived single chain antibodies. First, to produce unsecreted single chain antibodies (-IgK), a 773 bp fragment was obtained from pScFv9_E6VHlVk9 and pScFv9_E6VHVk9 by PCR introducing Xbal restriction site before the VH sequence and NotI at the end of the myc sequence. Digestion of the scAAV-CMV-EGFP (described in McCarty et al. Gene Ther.
  • pscAAV plasmids were digested with Hindlll and Pstl and the IgK sequence was inserted to obtain pscAAV_E6VHlVk9 and E6VH7Vk9 with a secretion signal.
  • the secreted single chain antibodies were obtained by a standard method (Rabinowitz et al. J Virol., 76: 791-801(2002)). Briefly, the fragment encompassing the ScFv expression cassette in pscFv9-E6VHl Vk9 and E6VH7Vk9 was excised using Hindlll and EcoRV and cloned into the plasmid Bluescript SK(-) (Stratagene, Canada).
  • EXAMPLE 13 E6 scFv antibodies reduce TDP-43 insolubility in ethacrynic acid-treated cells
  • Hek293 cells were transfected 72h in Optimem with 2 ⁇ g DNA and 5 ⁇
  • Lipofectamine 2000 reagent (Invitrogen) with E6 VI and E6 V7 scFv antibodies, empty plasmid or anti D1.3 scFv antibody and treated overnight with 50 ⁇ ethacrynic acid (EA) to induce TDP-43 aggregation, or treated overnight with same volume of DMSO diluent as a control.
  • the RIP A (radio- immunoprecipitation assay buffer) insoluble fraction was obtained.
  • a representative western blot is shown in Figure 12A and a representative dot blot analysis of TDP-43 is shown in Figure 12B.
  • EXAMPLE 14 E6 ScFv antibodies protect TDP-43 from Lysine
  • Hek293 cells were transfected 48h in Optimem with 2 ⁇ g DNA and 5 ⁇
  • Lipofectamine 2000 reagent (Invitrogen) with E6 scFv antibodies VI and V7, empty plasmid or anti D1.3 scFv antibody and treated for 4 hours with 50ng/ml TNF alpha.
  • Lysine acetylated proteins were immunoprecipitated using anti-acetyl-lysine antibody (Millipore) overnight in 300 ⁇ g total proteins lysate and the presence of lysine-acetylated TDP-43 was detected by western blotting for TDP-43 (Figure. 13). This result shows that that the E6 scFv antibodies protected TDP-43 from lysine acetylation.
  • TDP-43 acetylation impairs RNA-binding and promotes accumulation of insoluble, hyper-phosphorylated TDP-43 species that largely resemble pathological inclusions in ALS and FTLD-TDP (Cohen T.J., Hwang A.W., Restrepo C.R., et al. Nat Com 2014).

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Abstract

Provided herein are antigen-binding constructs such as antibodies that bind to the RRM-1 domain of TDP-43. The antigen-binding constructs are capable of blocking the interaction of TDP-43 with NF-κB in cells. Also provided herein are method of using the antigen-binding constructs in the treatment of diseases associated with TPD-43 proteinopathy, such as amyotrophic lateral sclerosis (ALS), frontotemperal lobar degeneration (FTLD), Lewy body disease and motor neuron disease.

Description

TDP-43 -BINDING POLYPEPTIDES USEFUL FOR THE TREATMENT OF
NEURODEGENERATIVE DISEASES
[0001] This application relates to TDP43 (TAR DNA-binding protein of 43 kDA)-specific binding constructs such as antibodies and fragments thereof that specifically bind to TDP- 43. The application also relates to methods of using the TDP-43 -binding polypeptides in the diagnosis and treatment of diseases characterized by TDP-43 proteinopathy such as amyotrophic lateral sclerosis, Azheimer's disease, motor neuron disease, Parkinson's disease and frontotemporal lobar degeneration. [0002] Neurodegenerative diseases are characterized by selective neurodegeneration in specific regions of the brain and spinal cord. Amyotrophic Lateral Sclerosis (ALS), commonly known as "Lou Gehrig's disease", is a progressive neurodegenerative disease of unknown etiology. The disease progressively impairs an individual's ability to control voluntary muscle movement. The disease tends to progress rapidly, leading to paralysis and death within 2-5 years of diagnosis in most cases.
[0003] A relatively recent discovery related to TDP-43 has provided fundamental insights into pathogenic mechanisms operative in ALS. TDP-43 was shown to be associated with the p65 sub-unit of the nuclear factor-κΒ (NF-κΒ) inflammation-regulating transcription factor in spinal cord samples obtained from ALS patients, but not from spinal cord sample of control patients (V. Swamp et al., 2011, J. Exp. Med., 208:2429-2447).
[0004] There are currently few therapeutic options for patients suffering from ALS. The only FDA approved drug for the treatment of ALS is Rilutek®, introduced in 1995, which extends life expectancy in individuals with ALS for a few months. There is therefore a need for new therapeutic approaches for neurodegenerative diseases such as ALS. [0005] As the symptoms of neurodegenerative diseases characterized by TDP-43 proteinopathy are similar to those of other neuromuscular disorders, diseases such as ALS is difficult to diagnose. The diagnosis is usually based on a complete neurological examination and clinical tests. There is therefore a need for methods and reagents for evaluating a subject predisposed to developing a neurodegenerative disease such as ALS and FTLD-U or suffering from these neurodegenerative diseases.
[0006] Provided herein are antigen-binding constructs that bind to TDP-43 (TAR DNA- binding protein of 43 kDa), such as antibodies, including fragments, derivatives and variants. In one embodiment, the antigen-binding constructs specifically bind to the RRM- 1 domain of TDP-43. In another embodiment, the antigen-binding constructs, when expressed in a cell, inhibits the binding of TDP-43 to the p65 subunit of NF-κΒ in the cell by at least 5%, 10%, 20%, 30%, 40%, 50% 50%, 70%, 80%, or 90%. In another embodiment, the antigen-binding constructs, when expressed in cells, attenuate the activation of NF-κΒ in response to LPS in the cells by at least 5%, 10%, 20%, 30%, 40%, 50% 50%), 70%), 80%), or 90%. In another embodiment, the antigen-binding constructs, when expressed in a cell, reduces the level of nuclear TDP-43 in the cell by at least 5%, 10%, 20%, 30%, 40%, 50% 50%, 70%, 80%, or 90%. In another embodiment, the antigen- binding constructs, when expressed in ethacrynic acid-treated Hek293 cells, reduce TDP- 43 insolubility by at least 5%, 10%, 20%, 30%, 40%, 50% 50%, 70%, 80%, or 90%. In another embodiment, the antigen -binding constructs, when expressed in Hek 293 cells incubated with TNF alpha, reduce the level of lysine acetylation of cellular TDP-43 by at least 5%, 10%, 20%, 30%, 40%, 50% 50%, 70%, 80%, or 90%. [0007] Provided herein are antigen-binding constructs that specifically bind to TDP-43 comprising at least one complementarity determining region (CDR) selected from the amino acid sequences set forth in (SEQ ID NO: 7), (SEQ ID NO: 8), (SEQ ID NO: 9), (SEQ ID NO: 10), (SEQ ID NO: 1 1), (SEQ ID NO: 12), (SEQ ID NO: 12), (SEQ ID NO: 14), (SEQ ID NO: 15), (SEQ ID NO: 16), (SEQ ID NO: 17), (SEQ ID NO: 18), (SEQ ID NO: 19), (SEQ ID NO: 20), (SEQ ID NO: 21), (SEQ ID NO: 22), (SEQ ID NO: 23) and (SEQ ID NO: 24).
[0008] Also provided herein are antigen-binding constructs that specifically bind to TDP- 43 comprising at least one heavy chain variable region VH comprising three VH complementarity determining regions (CDRs), wherein the VH comprises one, two or three of :
• a CDR selected from E6 VH1 CDR1, E6 VH7 CDR1, C10 VH3 CDR1 or C10 VH4 CDR1;
· a CDR selected from E6 VH1 CDR2, E6 VH7 CDR2, C10 VH3
CDR2 or C10 VH4 CDR2; and/or
• a CDR selected from E6 VH1 CDR3, E6 VH7 CDR3, C10 VH3 CDR3 or C10 VH4 CDR3.
[0009] In some embodiments, the antigen-binding construct comprises one, two or three VH CDRs that are at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to these VH CDRs. In some embodiments, the antigen-binding construct comprises the VH region of E6 VH1, E6 VH7, C10 VH3 or C10 VH4, or a VH region that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the VH of E6 VH1, E6_VH7, C10_VH3 or C10_VH4. [0010] In some embodiments, the antigen-binding construct further comprise a variable light chain region VL, wherein the VL comprises three VL CDRs, and wherein the VL comprises one, two or three of:
1. a CDR selected from E6_VK9 CDRl and C 10_VK3 CDRl ;
2. a CDR selected from E6_VK9 CDR2 and C10_VK3 CDR2; and/or 3. a CDR selected from E6_VK9 CDR3 or C 10_VK3 CDR3. as well as antigen-binding constructs comprising a CDR that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to these VL CDRs. In some embodiments, the antigen-binding construct comprises the VL of E6_VK9 or C10_VK3, or an antigen-binding construct having a VL that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the VL of E6_VK9 or C 10_VK3.
[0011] In some embodiments, the antigen binding construct comprises the VH region of E6 VH1 or E6 VH7 and the VL region of E6_VK9. In other embodiments, the antigen binding construct comprises the VH region of C10 VH3 or C10 VH4 and the VL region of C10_VK3. In other embodiments, the antigen-binding construct comprises the VH of E6 VH7 and the VL of E6_VK9, the VH of E6 VH1 and the VL of E6_VK9, the VH of C 10 VH3 and the VL of C 10_VK3 , or the VH of C 10 VH4 and the VL of C 10_VK3. [0012] In some embodiments, the antigen-binding construct comprises a peptide linker between the VH and VL, optionally the amino acid sequence SSGGGGSGGGGSGGGGS.
[0013] In some embodiments, the antigen-binding construct are E6_Vh7VK9, E6_Vhl VK9, C10_ VH3 VK3 or C10_ VH4VK3.
[0014] In some embodiments, the antigen-binding constructs comprise the six CDRs of E6_VH7VK9. In some embodiments, the antigen-binding constructs comprise the six CDRs of E6_VhlVK9. In some embodiments, the antigen-binding constructs comprise the six CDRs of C10_VH3VK3. In some embodiments, the antigen-binding constructs comprise the six CDRs of C10_VH4VK3.
[0015] In some embodiments, the TDP-43 antigen-binding construct comprises a secretory signal peptide. In a specific embodiment, the secretory signal peptide is M G D N D I H F A F L S T G V H S Q V Q. In some embodiments, the TDP-43 antigen-binding construct have an scFv format. In other embodiments, the TDP-43 antigen-binding constructs have an Fab format. In one embodiment, the TDP-43 antigen binding construct has a single domain antibody (camelid) format. In some embodiments, the TDP-43 antigen-binding construct has an (Fab')2 format. The TDP-43 antigen-binding constructs may also comprise an Fc domain. The antigen-binding constructs may also be humanized, or de-immunized.
[0016] Also encompassed herein are antigen-binding constructs that specifically bind to an RRM-1 domain of TDP-43, comprising a VH and a VL, such that the construct, when expressed in cells, reduces the interaction of an intracellular TDP-43 polypeptide with an intracellular F-κΒ p65 polypeptide, and/or reduces the activation of NF-κΒ in cells in response to LPS. In some embodiments, the interaction of intracellular TDP-43 polypeptide with intracellular NF-κΒ p65 polypeptide is reduced 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% or more. In some embodiments, the activation of F- KB in cells in response to LPS is reduced by 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% or more.
[0017] Also provided herein is an antigen-binding construct that blocks by 50%, 60%, 70%, 80% or 90% or more the binding of any of E6_VHlVk9, E6_VH7Vk9, C10_VH3Vk3 or C10_VH4Vk3 to either TDP-43 or to the RRM-1 domain of TDP-43.
[0018] Also described herein are pharmaceutical compositions comprising the antigen- binding construct described above, and pharmaceutically acceptable excipient.
[0019] Also described are methods of treating or preventing a disease or disorder characterized by TDP-43 proteinopathy in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of the TDP-43 antigen- binding constructs provided herein.
[0020] Provided herein are methods of treating or preventing a disease or disorder characterized by TDP-43 proteinopathy in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an adeno-associated viral (AAV) vector comprising at least one nucleic acid sequence that encodes at least one TDP- 43 antigen-binding construct.
[0021] Provided herein is a use of the antigen-binding constructs as defined herein for the manufacture of a medicament for the treatment or prevention of a disease or disorder characterized by TDP-proteinopathy.
[0022] Provided herein is a use of the antigen-binding constructs as described herein for the treatment or prevention of a disease or disorder characterized by TDP-proteinopathy.
[0023] In some embodiments, the disease or disorder being treated is amyotrophic lateral sclerosis (ALS), Alzheimer's disease, motor neuron disease, Parkinson's disease, frontotemperal lobar degeneration (FTLD), mild cognitive impairment (MCI), Lewy body disease, brain trauma or cerebral ischemia. [0024] Also provided are methods of producing the antigen-binding constructs comprising culturing a host cell under conditions suitable for expressing the antigen-binding construct, wherein the host cell comprises a polynucleotide encoding a TDP-43 antigen binding construct, and purifying the construct. [0025] Also provided herein are polynucleotide or set of isolated polynucleotides comprising at least one nucleic acid sequence that encodes at least one of the TDP-43 antigen-binding constructs. In one embodiment, the polynucleotide is a cDNA.
[0026] Also described herein is vector or set of vectors comprising one or more of the polynucleotides or sets of polynucleotides encoding the antigen-binding constructs. [0027] In some embodiments, the vector is a plasmid, a viral vector, a non-episomal mammalian vector, an expression vector, and a recombinant expression vector. In a specific embodiment, the vector is an adeno-associated viral (AAV) vector. Also described is an isolated host cell comprising one or more polynucleotides encoding TDP-43 antigen binding constructs. [0028] Figure 1 is an immunoblot of nuclear extracts of BV-2 cells that were fractionated by SDS-PAGE and treated with three exemplary monocloncal anti-TDP-43 antibodies, CIO, G8 and E6, raised against the RRMI domain of TDP-43. The three antibodies detected TDP-43 in nuclear extracts of BV-2 cells that were stimulated with LPS or not.
[0029] Figure 2 is a bar graph showing the results of an ELISA assay demonstrating that human recombinant p65_His-Tag directly interacts with human recombinant TDP-43 GST Tag. The results are shown as the Absorbance (ABS) at 450 nm read for varying concentrations amount of human recombinant TDP-43 added to the assay from 0.01 to 0.8
[0030] Figure 3 is a bar graph showing the results of an ELISA assay demonstrating that interaction between recombinant TDP-43 and F-κΒ p65 is blocked by exemplary monoclonal anti-TDP-43 antibodies CIO, G8, and E6. The results are shown as the Absorbance (ABS) at 450 nm read for the different recombinant anti-TDP-43 antibodies. [0031] Figure 4 is a schematic representation of vectors encoding exemplary anti-TDP-43 scFv antibodies. The scFv vectors were constructed in a VH-linker-VK format together with a flexible 20-amino acid linker (Gly4Ser)3. The scFv constructs contain a murine immunoglobulin (Ig) κ-secretory signal for efficient secretion and a human c-myc epitope 5 to facilitate detection.
[0032] Figure 5 is an immunoblot of an SDS PAGE gel of nuclear and cytoplasmic fractions of Hek293 cells transfected with an ScFv9 expression plasmids encoding anti- TDP-43 antigen-binding constructs E6 VH1 VK9 and E6_VH7VK9.
[0033] Figure 6 is a dot blot showing that the E6_VH1VK9 and E6_VH7VK9 antigeni c) binding constructs bind to amino acids 1-206 of TDP-43.
[0034] Figure 7 shows the results of an ELISA assay demonstrating that exemplary anti- TDP-43 antibodies E6_VH1VK9 and E6_VH7VK9 having an scFv format block the interaction between recombinant TDP-43 and F-κΒ p65.
[0035] Figure 8 shows that an exemplary anti-TDP-43 antibody E6_VH1VK9 in an scFv 15 format co-immunoprecipitate with TDP-43 as detected by polyclonal antibodies against TDP-43. (expressed into the medium of Hek293 cells following transfection with ScFv9 expression plasmids encoding E6 VH1 VK9).
[0036] Figure 9 shows that exemplary anti-TDP-43 antibody E6_VH1VK9 having an scFv format blocks the interaction of TDP-43 with NF-κΒ p65 in Hek293 cells. This was 0 revealed by an assay in which cell extracts from Hek293 cells expressing E6_VH1VK9 were immunoprecipitated with anti-TDP-43 polyclonal antibodies, revealing a decreased level of NF-κΒ p65 for cells expressing VHl VK9 compared to cells transfected with an empty ScFv9 expression vector.
[0037] Figure 10 shows the ability of expression vectors encoding exemplary scFv 5 antibodies against TDP-43 to attenuate NF-κΒ activity in response to LPS as measured by a NF-KB -luciferase reporter construct stably integrated into BV2 microglial cells. [0038] Figure 11 shows the reduction in levels of nuclear TDP-43 caused by expression of scFv anti-TDP-43 antibodies in Neuro2A cells.
[0039] Figure 12 shows the ability of anti-TDP-43 antibody to reduce TDP-43 insolubility in E6_VH1VK9 and E6_VH7VK9 transfected Hek293 cells treated with ethacrynic acid. (A) shows a western blot. (B) shows a dot blot analysis.
[0040] Figure 13 shows the ability of anti-TDP-43 antibodies to protect TDP-43 from lysine acetylation in E6 VH1 VK9 and E6_VH7VK9 transfected Hek293 cells.
[0041] Disclosed herein are TDP-43 -binding constructs and their uses in the diagnosis and therapy of neurodegenerative diseases characterized by TDP-43 proteinopathy. TDP-43
[0042] As used herein, the terms "TDP43," refers to transactivation responsive-DNA binding protein of 43kDa, or TAR-DNA binding protein of 43kDA, and is used to refer to all types and forms of TPD-43, including the native form as well as other conform ers of TDP- 43, including for example, phosphorylated forms of TDP-43, aggregates of TDP-43, ubiquitin-associated aggregates of TDP-43 and TDP-43 variants that have one or more mutations compared to native TDP-43, and pathogenic forms. TDP-43 also includes fragments of TDP-43 polypeptide. TDP-43 is a DNA/RNA-binding protein that contains an N-terminal domain, two RNA-recognition motifs and a glycine-rich C-terminal domain thought to be important for mediating protein-protein interactions The amino acid sequence of human TDP-43 is known in the art; see, e.g., Strausberg et al., TARDBP protein (Homo sapiens) GenBank Pubmed: An amino acid sequence of human TDP 43 is shown in AAH71657 version GL47939520 herein incorporated by reference in its entirety. The amino acid sequence of native human TDP-43 is as shown below and in Table A (SEQ ID NO: 29). The RRMl domain corresponds to amino acids 101 to 176. 1 MSEYIRVTED ENDEPIEIPS EDDGTVLLST VTAQFPGACG LRYRNPVSQC MRGVRLVEGI 61 LHAPDAGWGN LVYVVNYPKD NKRKMDETDA SSAVKVKRAV QKTSDLIVLG LPWKTTEQDL
121 KEYFSTFGEV LMVQVKKDLK TGHSKGFGFV RFTEYETQVK VMSQRHMIDG RWCDCKLPNS
181 KQSQDEPLRS RKVFVGRCTE DMTEDELREF FSQYGDVMDV FIPKPFRAFA FVTFADDQIA
241 QSLCGEDLII KGISVHISNA EPKHNSNRQL ERSGRFGGNP GGFGNQGGFG NSRGGGAGLG
301 NNQGSNMGGG MNFGAFSINP AMMAAAQAAL QSSWGMMGML ASQQNQSGPS GNNQNQGNMQ
361 REPNQAFGSG NNSYSGSNSG AAIGWGSASN AGSGSGFNGG FGSSMDSKSS GWGM (SEQ ID
NO: 49) NF-kB p65
[0043] As used herein the term " FkB p65 or " FKB" refers to nuclear factor kappa B, and "NF-kB p65" or "p65" are used interchangeably herein to refer to the p65 subunit or chain of NFkB p65. p65 polypeptides as well as polynucleotides are known in the art. For example see NCBI M62399.1. An amino acid sequence for human NF-κΒ p65 is shown below. Reference to p65 herein also includes fragments of p65.
MDELFPLIFPAEPAQASGPYVEIIEQPKQRGMRFRYKCEGRSAG
SIPGERSTDTTKTHPTIKINGYTGPGTVRISLVTKDPPHRPHPHELVGKDCRDGFYEA ELCPDRCIHSFQNLGIQCVKKRDLEQAISQRIQTNNNPFQVPIEEQRGDYDLNAVRLC FQVTVRDPSGRPLRLPPVLPHPIFDNRAPNTAELKICRVNRNSGSCLGGDEIFLLCDK VQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPYADPSLQAPVRVSMQLRRPS DRELSEPMEFQYLPDTDDRHRIEEKRKRTYETFKSIMKKSPFSGPTDPRPPPRRIAVP SRSSASVPKPAPQPYPFTSSLSTINYDEFPTMVFPSGQISQASALAPAPPQVLPQAPA PAPAPAMVSALAQAPAPVPVLAPGPPQAVAPPAPKPTQAGEGTLSEALLQLQFDDEDL GALLGNSTDPAVFTDLASVDNSEFQQLLNQGIPVAPHTTEPMLMEYPEAITRLVTGAQ RPPDPAPAPLGAPGLPNGLLSGDEDFSSIADMDFSALLSQISS(SEQ ID NO: 50)
Neurodegenerative diseases characterized by TDP-43 proteinopathy
[0044] The term "TDP-43 proteinopathy" relates to the nervous system diseases, in particular to neurodegenerative diseases, and are known as a heterologous group of disorders linked by association with TDP-43 abnormalities, and particularly with accumulation and/or aggregation of abnormal or misfolded TDP-43 polypeptides. TDP proteinopathies include, but are not limited to amyotrophic lateral sclerosis (ALS), Parkinson's disease, frontotemporal lobar degeneration (FTLD) motor neuron disease, Alzheimer's disease, dementia with Lewy bodies, Huntington's disease, or Lewy body disease. Abnormal TDP-43 accumulations may also be triggered by nerve injury, brain trauma, brain ischemia (stroke).
[0045] The term "frontotemporal lobar degeneration disease" refers to a group of disorders associated with atrophy in the frontal and temporal lobes. Frontotemporal lobar degeneration disease (FTLD) can include FTLD-tau characterized by tau inclusion, FTLD- TDP43 characterized by ubiquitin and TDP-43 inclusion (FTLD-U), FTLD-FUS characterized by FUS cytoplasmic inclusions and dementia lacking distinctive histology (DLDH). [0046] The term "amyotrophic lateral sclerosis" (ALS) is used herein to refer to any neurodegenerative disease that usually attacks both upper and lower motor neurons and causes degeneration throughout the brain and spinal cord.
Antigen binding constructs
[0047] Described herein are antigen-binding constructs that bind to TDP-43 (TAR DNA- binding protein of 43 kDa), such as antibodies, including fragments, derivatives and variants of antibodies that are capable of specifically binding to TDP-43. By "specifically binding to TDP-43", "antibody specific to/for TDP-43" and "anti-TDP-43 antibody" and "TDP-43 antibody" is meant specifically, generally, and collectively, antibodies to TDP- 43, or misfolded or oligomeric or aggregated or posttranslationally modified TDP-43 or variants of TDP-43. According to one embodiment, antibodies as described herein (including antigen-binding antibody fragments and derivatives) specifically binds to the RRM-1 domain of TDP- 43. In one embodiment, the TDP-43 specific antigen binding construct is an antibody (including antigen-binding fragments or derivatives thereof) having an immunological binding characteristic of the antibodies described herein. In some embodiments, the antigen-binding constructs block the binding of TPD-43 to NF-KB p65.
[0048] Described herein are antigen-binding constructs that specifically bind to TDP-43 comprising at least one heavy chain variable region VH comprising three VH complementarity determining regions (CDRs), wherein the VH comprises one, two or three of:
• a CDR selected from E6 VH1 CDR1, E6 VH7 CDR1, C10 VH3 CDR1 or C10 VH4 CDR1;
· a CDR selected from E6 VH1 CDR2, E6 VH7 CDR2, C10 VH3
CDR2 or C10 VH4 CDR2; and/or
• a CDR selected from E6 VH1 CDR3, E6 VH7 CDR3, C10 VH3 CDR3 or C10 VH4 CDR3.
[0049] In some embodiments, the antigen-binding construct comprises one, two or three VH CDRs that are at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the those VH CDRs. In some embodiments, the antigen-binding construct comprises the VH of E6 VH1, E6_VH7, C10_VH3 or C10_VH4, or a VH that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the VH of E6 VH1, E6_VH7, C10_VH3 or C10 VH4. [0050] In some embodiments, the antigen-binding construct of further comprising a variable light chain region VL, wherein the VL comprises three VL CDRs, and wherein the VL comprises one, two or three of:
• a CDR selected from E6_VK9 CDRl and C 10_VK3 CDRl ;
• a CDR selected from E6_VK9 CDR2 and C10_VK3 CDR2; and/or · a CDR selected from E6_VK9 CDR3 or C 10_VK3 CDR3 ; as well as antigen-binding constructs comprising a CDR that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to those VL CDRs. In some embodiments, the antigen-binding construct comprises the VL of E6_VK9 or C10_VK3, or an antigen-binding construct having a VL that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the VL of E6 VK9 or C10 VK3. [0051] In some embodiments, the antigen binding construct comprises the VH region of E6 VH1 or E6 VH7 and the VL region of E6_ VK9. In other embodiments, the antigen binding construct comprises the VH region of C10 VH3 or C10 VH4 and the VL region of C10_ VK3. In other embodiments, the antigen-binding construct comprises the VH of E6 VH7 and the VL of E6_VK9, the VH of E6 VH1 and the VL of E6_VK9, the VH of C 10 VH3 and the VL of C 10_VK3 , or the VH of C 10 VH4 and the VL of C 10_ VK3.
[0052] In some embodiments, the antigen-binding construct comprises the six CDRs selected from:
(a) the CDR1 (SEQ ID NO. 7), CDR2 (SEQ ID NO. 8) and CDR3 (SEQ ID NO. 9), of E6 VH1 and the CDR1 (SEQ ID NO. 7), CDR2 (SEQ ID NO. 8) and CDR3 (SEQ ID
NO. 9) of E_6VK9;
(b) the CDR1 (SEQ ID NO. 10), CDR2 (SEQ ID NO. 11) and CDR3 (SEQ ID N012) of E6 VH7 and the CDR1 (SEQ ID NO. 7), CDR2 (SEQ ID NO. 8) and CDR3 (SEQ ID NO. 9) of E_6VK9;
(c) the CDR1 (SEQ ID NO 16), CDR2 (SEQ ID NO. 17) and CDR3 (SEQ ID NO.
18) of C10 VH3, and the CDR1 (SEQ ID NO. 22), CDR2 (SEQ ID NO. 23 and CDR3
(SEQ ID NO. 24) of C10_VK3;
(d) the CDR1 (SEQ ID NO 19), CDR2 (SEQ ID NO. 20) and CDR3 (SEQ ID NO.
21) of C10 VH4 and the CDR1 (SEQ ID NO. 22), CDR2 (SEQ ID NO. 23 and CDR3 (SEQ ID NO. 24) of C10_VK3.
[0053] In some embodiments, the antigen-binding construct comprises a peptide linker between the VH and VL, optionally the amino acid sequence SSGGGGSGGGGSGGGGS.
[0054] In some embodiments, the antigen-binding construct comprises E6_Vh7VK9, E6_VhlVK9, C10_VH3VK3 or C10_VH4VK3.
[0055] In some embodiments, the antigen-binding construct comprises a secretory signal peptide. In a specific embodiment, the secretory signal peptide is M G D N D I H F A F L S T G V H S Q V Q. [0056] In some embodiments, the antigen-binding construct have an scFv format. In other embodiments, the antigen-binding constructs have an Fab format. In one embodiment, the antigen binding construct has a single domain antibody (for example, a camelid) format. In some embodiments, the antigen-binding construct has an (Fab')2 format. In another embodiment, the antigen-binding construct has an Fab' format. The antigen-binding constructs may also comprise an Fc domain. The antigen-binding constructs may also be humanized, or de-immunized.
[0057] Also provided herein are antigen-binding constructs that specifically bind to an RRM-1 domain of TDP-43, comprising a VH and a VL, such that the construct, when expressed in cells, reduces the interaction of an intracellular TDP-43 polypeptide with an intracellular F-κΒ p65 polypeptide and/or reduces the activation of NF-κΒ in cells in response to LPS. In some embodiments, the interaction of intracellular TDP-43 polypeptide with intracellular F-κΒ p65 polypeptide is reduced 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% or more. In some embodiments, the activation of F- KB in cells in response to LPS is reduced by 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% or more.
[0058] Also provided herein are antigen-binding constructs that specifically bind to an RRM-1 domain of TDP-43, comprising a VH and a VL, wherein the construct, when expressed in a cell, i) reduces the interaction of an intracellular TDP-43 polypeptide with an intracellular F-κΒ p65 polypeptide in Hek293 cells by 10% or more; or
ii) reduces the activation of F-κΒ in the BV-2 cells in response to LPS by 10%) or more; or
iii) reduces the level of nuclear TDP-43 in Neuro2A cells; or iv) reduces the lysine acetylation of TDP-43 in Hek293 cells in response to TNF alpha by 10% or more; or v) reduces the insolubility of TDP-43 in Hek293 cells incubated with ethacrynic acid.
[0059] Also provided herein are antigen-binding construct that blocks by 50%, 60%, 70%, 80% or 90% or more the binding of any of E6_VHlVk9, E6_VH7Vk9, C10_VH3Vk3 or C10_VH4Vk3 to either TDP-43 or to the RRM-1 domain of TDP-43. In some embodiments, the antigen-binding construct blocks the binding of any of E6 VH1 Vk9, E6_VH7Vk9, C10_VH3Vk3 or C10_VH4Vk3 to either TDP-43 or to the RRM-1 domain of TDP-43 by 50% or more.
[0060] The term "antigen binding construct" also refers to any agent, e.g., polypeptide or polypeptide complex capable of binding to an antigen. In some aspects an antigen binding construct is a polypeptide the specifically binds to an antigen of interest. An antigen binding construct can be a monomer, dimer, multimer, a protein, a peptide, or a protein or peptide complex; an antibody, an antibody fragment, or an antigen binding fragment thereof; an scFv and the like. An antigen binding construct can be a polypeptide construct that is monospecific, bispecific, or multispecific. In some aspects, an antigen binding construct can include, e.g., one or more antigen binding components (e.g., Fabs or scFvs) linked to one or more Fc. Further examples of antigen binding constructs are described below and provided in the Examples.
[0061] The term "bispecific" is intended to include any agent, e.g., an antigen binding construct or antibody, which has two different binding specificities.
[0062] The term "multispecific" or "heterospecific" is intended to include any agent, e.g., an antigen binding construct or antibody, which has two or more different binding specificities. Accordingly, embodiments of the antigen-binding constructs described herein, are inclusive of, but not limited to, bispecific, trispecific, tetraspecific, and other multispecific molecules.
[0063] An antigen binding construct can be an antibody or antigen binding portion thereof. As used herein, an "antibody" or "immunoglobulin" refers to a polypeptide substantially encoded by an immunoglobulin gene or immunoglobulin genes, or fragments thereof, which specifically bind and recognize an analyte (e.g., antigen). The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. The "class" of an antibody or immunoglobulin refers to the type of constant domain or constant region possessed by its heavy chain. There are five major classes of antibodies: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgGi, IgG2, IgG3, IgG4, IgAi, and IgA2. The heavy chain constant domains that correspond to the different classes of immunoglobulins are called α, δ, ε, γ, and μ, respectively.
[0064] An exemplary immunoglobulin (antibody) structural unit is composed of two pairs of polypeptide chains, each pair having one "light" (about 25 kD) and one "heavy" chain (about 50-70 kD). The N-terminal domain of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (VH) refer to these light and heavy chain domains respectively. The IgGl heavy chain comprises the VH, CHI, CH2 and CH3 domains respectively from the N to C-terminus. The light chain comprises the VL and CL domains from N to C terminus. The IgGl heavy chain comprises a hinge between the CHI and CH2 domains. In certain embodiments, the immunoglobulin constructs comprise at least one immunoglobulin domain from IgG, IgM, IgA, IgD, or IgE connected to a therapeutic polypeptide. In some embodiments, the immunoglobulin domain found in an antigen binding construct provided herein, is from or derived from an immunoglobulin based construct such as a diabody, or a nanobody. In certain embodiments, the immunoglobulin constructs described herein comprise at least one immunoglobulin domain from a heavy chain antibody such as a camelid antibody. In certain embodiments, the immunoglobulin constructs provided herein comprise at least one immunoglobulin domain from a mammalian antibody such as a bovine antibody, a human antibody, a camelid antibody, a mouse antibody or any chimeric antibody. [0065] The term "hypervariable region" or "HVR", as used herein, refers to each of the regions of an antibody variable domain which are hypervariable in sequence and/or form structurally defined loops ("hypervariable loops"). Generally, native four-chain antibodies comprise six HVRs; three in the VH (HI, H2, H3), and three in the VL (LI, L2, L3). HVRs generally comprise amino acid residues from the hypervariable loops and/or from the complementarity determining regions (CDRs), the latter being of highest sequence variability and/or involved in antigen recognition. With the exception of CDR1 in VH, CDRs generally comprise the amino acid residues that form the hypervariable loops. Hypervariable regions (HVRs) are also referred to as "complementarity determining regions" (CDRs), and these terms are used herein interchangeably in reference to portions of the variable region that form the antigen binding regions. This particular region has been described by Kabat et al., U.S. Dept. of Health and Human Services, Sequences of Proteins of Immunological Interest (1983) and by Chothia et al., J Mol Biol 196:901-917 (1987), where the definitions include overlapping or subsets of amino acid residues when compared against each other. Nevertheless, application of either definition to refer to a CDR of an antibody or variants thereof is intended to be within the scope of the term as defined and used herein. The exact residue numbers which encompass a particular CDR will vary depending on the sequence and size of the CDR. Those skilled in the art can routinely determine which residues comprise a particular CDR given the variable region amino acid sequence of the antibody.
[0066] An "Fab molecule" or a "Fab" refers to a protein or polypeptide construct consisting of the VH and CHI domain of the heavy chain (the "Fab heavy chain") and the VL and CL domain of the light chain (the "Fab light chain") of an immunoglobulin. A Fab is monovalent. [0067] An "F(ab')2" molecule refers to a protein or polypeptide construct consisting of two Fabs linked together by part of a hinge region, but is missing the most of the Fc. An F(ab')2 molecule may be obtained by digesting an immunoglobulin with papain or pepsin.
[0068] As used herein, the term "single-chain" refers to a molecule comprising amino acid monomers linearly linked by peptide bonds. In certain embodiments, one of the antigen binding moieties is a single-chain Fab molecule, i.e. a Fab molecule wherein the Fab light chain and the Fab heavy chain are connected by a peptide linker to form a single peptide chain. In a particular such embodiment, the C-terminus of the Fab light chain is connected to the N-terminus of the Fab heavy chain in the single-chain Fab molecule. In certain other embodiments, one of the antigen binding moieties is a single-chain Fv molecule (scFv). As described in more detail herein, an "scFv" has a variable domain of light chain (VL) connected from its C-terminus to the N-terminal end of a variable domain of heavy chain (VH) by a polypeptide chain, or alternately the the C-terminal end of the VH is connected to the N-terminal end of VL by a polypeptide chain. Antibodies of this type are referred to herein as having an "scFv format".
[0069] In some embodiments described herein, an scFv format is used in an antigen- binding construct (i.e. antigen -binding domains composed of a heavy chain variable domain and a light chain variable domain). In one embodiment said scFv molecules are human. In another embodiment said scFv molecules are humanized. In one embodiment said scFv molecules are murine. The variable regions may be connected directly or, typically, via a linker peptide that allows the formation of a functional antigen-binding moiety. Typical peptide linkers comprise about 2-20 amino acids, and are described herein or known in the art. Suitable, non-immunogenic linker peptides include, for example, (G4S)n, (SG4)n, (G4S)n, G4(SG4)n or G2(SG2)n linker peptides, wherein n is generally a number between 1 and 10, typically between 2 and 4. The scFv molecule may be further stabilized by disulfide bridges between the heavy and light chain variable domains, for example as described in Reiter et al. (Nat Biotechnol 14, 1239-1245 (1996)). As is known in the art, scFvs can also be stabilized by mutation of CDR sequences, as described in [Miller et al., Protein Eng Des Sel. 2010 Jul;23(7):549-57; Igawa et al., MAbs. 2011 May- Jun;3(3):243-5; Perchiacca & Tessier, Annu Rev Chem Biomol Eng. 2012;3 :263-86.]. In some embodiments, an TDP-43 antigen-binding construct in an scFv format is preferred for its ability to cross cell membranes and enter cells. A schematic representation of an scFv format antibody is shown in Figure 4B. [0070] In some embodiments, a TDP-43 antigen-binding construct may consist of a single VH polypeptide (camelid format).
[0071] By a "crossover" Fab molecule (also termed "Crossfab") is meant a Fab molecule wherein either the variable regions or the constant regions of the Fab heavy and light chain are exchanged, i.e. the crossover Fab molecule comprises a peptide chain composed of the light chain variable region and the heavy chain constant region, and a peptide chain composed of the heavy chain variable region and the light chain constant region. For clarity, in a crossover Fab molecule wherein the variable regions of the Fab light chain and the Fab heavy chain are exchanged, the peptide chain comprising the heavy chain constant region is referred to herein as the "heavy chain" of the crossover Fab molecule. Conversely, in a crossover Fab molecule wherein the constant regions of the Fab light chain and the Fab heavy chain are exchanged, the peptide chain comprising the heavy chain variable region is referred to herein as the "heavy chain" of the crossover Fab molecule.
[0072] "Framework" or "FR" refers to variable domain residues other than hypervariable region (HVR) residues. The FR of a variable domain generally consists of four FR domains: FR1 , FR2, FR3, and FR4. Accordingly, the HVR and FR sequences generally appear in the following sequence in VH (or VL): FR1-H1(L1)-FR2-H2(L2)-FR3-H3(L3)- FR4.
[0073] The antigen-binding constructs may comprise an Fc region or domain, e.g., a dimeric Fc.
[0074] The term "Fc domain" or "Fc region" herein is used to define a C-terminal region of an immunoglobulin heavy chain that contains at least a portion of the constant region. The term includes native sequence Fc regions and variant Fc regions. Unless otherwise specified herein, numbering of amino acid residues in the Fc region or constant region is according to the EU numbering system, also called the EU index, as described in Kabat et al, Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD, 1991. A "subunit" of an Fc domain as used herein refers to one of the two polypeptides forming the dimeric Fc domain, i.e. a polypeptide comprising C-terminal constant regions of an immunoglobulin heavy chain, capable of stable self-association. For example, a subunit of an IgG Fc domain comprises an IgG CH2 and an IgG CH3 constant domain.
[0075] In some aspects, the Fc comprises at least one or two CH3 sequences. In some aspects, the Fc is a homodimeris Fc. In some aspects the Fc is heterodimeric FC. In some aspects, the Fc is a human Fc. In some aspects, the Fc is a murine Fc. In some aspects, the Fc is a human IgG or IgGl Fc. In some aspects, the Fc comprises at least one or two CH2 sequences.
[0076] In some aspects, the Fc comprises one or more modifications in at least one of the CH3 sequences. In some aspects, the Fc comprises one or more modifications in at least one of the CH2 sequences. In some aspects, an Fc is a single polypeptide. In some aspects, an Fc is multiple peptides, e.g., two polypeptides.
[0077] Fused or linked means that the components (e.g. a Fab molecule or an scFv molecule and an Fc domain subunit) are linked by peptide bonds, either directly or via one or more peptide linkers.
[0078] Antigen-binding constructs bind antigen. As used herein, the term "antigenic determinant" is synonymous with "antigen" and "epitope," and refers to a site (e.g. a contiguous stretch of amino acids or a conformational configuration made up of different regions of non-contiguous amino acids) on a polypeptide macromolecule to which an antigen-binding moiety binds, forming an antigen-binding moiety-antigen complex. The antigen bound by the antigen-binding constructs described herein is TPD-43, and in some embodiments, the RRM-1 domain of TDP-43.
[0079] "Specifically binds", "specific binding" or "selective binding" means that the binding is selective for the antigen and can be discriminated from unwanted or non-specific interactions. The ability of an antigen-binding moiety to bind to a specific antigenic determinant can be measured either through an enzyme-linked immunosorbent assay (ELISA) or other techniques familiar to one of skill in the art, e.g. surface plasmon resonance (SPR) technique (analyzed on a BIAcore instrument) (Liljeblad et al, Glyco J 17, 323-329 (2000)), and traditional binding assays (Heeley, Endocr Res 28, 217-229 (2002)). In one embodiment, the extent of binding of an antigen-binding moiety to an unrelated protein is less than about 10% of the binding of the antigen-binding moiety to the antigen as measured, e.g., by SPR. In certain embodiments, an antigen-binding moiety that binds to the antigen, or an antigen-binding molecule comprising that antigen-binding moiety, has a dissociation constant (KD) of < 1 μΜ, < 100 nM, < 10 nM, < 1 nM, < 0.1 nM, < 0.01 nM, or < 0.001 nM (e.g. 10~8 M or less, e.g. from 10~8 M to 10"13 M, e.g., from 10"9 M to 10"13 M). [0080] An antibody "which binds" an antigen of interest is one capable of binding that antigen with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent.
[0081] "Affinity" refers to the strength of the sum total of non-covalent interactions between a single binding site of a molecule (e.g., a receptor) and its binding partner (e.g., a ligand). Unless indicated otherwise, as used herein, "binding affinity" refers to intrinsic binding affinity which reflects a 1 : 1 interaction between members of a binding pair (e.g., an antigen-binding construct and an antigen, or a receptor and its ligand). The affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (KD), which is the ratio of dissociation and association rate constants (k0ff and kon, respectively). Thus, equivalent affinities may comprise different rate constants, as long as the ratio of the rate constants remains the same. Affinity can be measured by well-established methods known in the art, including those described herein. A particular method for measuring affinity is Surface Plasmon Resonance (SPR).
[0082] The antigen-binding constructs described herein include at least one antigen- binding polypeptide that binds TDP-43. Table A shows the amino acid sequences of exemplary anti-TDP-43 antigen binding polypeptides. ( ) = Igk secretory signal; { } = linker sequence; [ ] = c-myc detection signal. [0083] Also provided herein are nucleic acid sequences encoding the exemplary antigen- binding constructs. Table B shows these exemplary nucleic acid sequences.
Figure imgf000023_0001
E6 VK9 CDR3 KQ S YNL YT
CIO VH3 CDR1 S S F G Met H W
CIO VH3 CDR2 YI SSGS STLHYAD
CIO VH3 CDR3 FL QMetKLP SL
CIO VH4 CDR1 S S F G Met H W
CIO VH4 CDR2 YI SSGS STLHYAD
CIO VH4 CDR3 FL QMetKLP SL
CIO VK3 CDRl RASKSVST SGYSY Met H
CIO VK3 CDR2 YL VSNLES
CIO VK3 CDR3 QHIREL TR
E6_VH1VK9 complete (MGDNDIHFAFLSTGVHSOVO! LOESGGGLVOPGG with IGk secretory S Met KLSCVASGFTSSNYWLNWVRQSPERGLE
WVAEIRLKSNNYATNYAESVKGRFTISRDDSK
signal and c-myc SSVYLQVNNLRAEDTGIYYCTRSTARATPYYF peptide DYWGOGTTVTVSSGG{GGSGGGGSGGGGSDI}ELT
QSPSSLAVSAGEKVT Met SCKSSQSLLNSRARK NFLTWYQQKPGQSPKLLIYWASTRESGVPDR FTGSGSGTDFTLTISSVQAEDLAVYYCKQSYN LYTFGGGTKLE [EOKLISEEDLNl
E6_VH1VK9 full LQESGGGLVQPGGS Met KLSCVASGFTSSNYW
LNWVRQSPERGLEWVAEIRLKSNNYATNYAE
SVKGRFTISRDDSKSSVYLQVNNLRAEDTGIY
YCTRSTARATPYYFDYWGOGTTVTVSSGG{GGS
GGGGSGGGGSDIjELTOSPS SLAVS AGEKVTMetS
CKSSQSLLNSRARKNFLTWYQQKPGQSPKLL
IYWASTRESGVPDRFTGSGSGTDFTLTISSVQ
AEDLAVYYCKQSYNLYTFGGGTKLE
E6_VH7VK9 complete fMGDNDIHFAFLSTGVHSOVO! LQQS G G G LVQ P G with IGk secretory G S Met KLS CVAS G FTSS N YWL NWVRQS P E RG signal and c-myc L EWVA E I R L KS N N YAT NYA E SVKG R F TI S RD peptide DS KS SVY LQVN N L RA E DTG I YYCTRSTA RAT
PYY F DYWG QG TTVTV{SSGGGGSGGGGSGGGGSD
] E LTQS PSS LAVSA G E KVT Met S C KSS QS L L N
S RA R KN F LTWYQQ KP G QS P K L LI YWA ST RE
S GVP D R FTG S G S G TD FT LTI SSVQA E D LAVY
YC KQSY N LYTF G G G T KL E [EOKLISEEDLN]
E6_VH7VK9 full LQQS G G G LVQ P G G S Met KLS CVAS G FTSS N Y
WL NWVRQS P E RG L EWVA E I RL KS N N YATN Y A E SVKG RFTI S R D DS KS SVY LQVN N L RA E DT G I YYCT RSTA RATPYYF DYWG QG TTVTV{SSG GGGSGGGGSGGGGSDI}E LTQS P SS LAVSA G E KV T Met S C KSS QS L L N S RA R KN F LTWYQQ KP G Q S P K L LI YWAST RE S GVP D R FTG S G S G TD FT L TI SSVQA E D LAVYYC KQSYN LYT F G G G TK L E
C10_VH3VK3 complete ("MGDNDIHFAFLSTGVHSOVOI LQE S G G G LVQ PG
G S RK LS CAAS G FT FSS F G Met HWVRQA P E KG with IGk secretory LEWVAYISSGSSTLHYADTVKG RFTISRDN P signal and c-myc K N T L F L Q Met KLPS LCYG LLG PRDHG H{SSGGG peptide GSGGGGSGGGGSJELTQSPASLAVSLGQRATISY
RASKSVSTSGYSY Met HWNQQKPGQPP RLLI
YLVSN LESGVPARFSGSGSGTDFTLNI H PVE
EEDAATYYCQHI RELTRS EGAPSSfEOKLISEE
DLN]
C10_VH3VK3 full LQESGGG LVQPGGSRKLSCAASG FTFSSF
G Met HWVRQAP EKG LEWVAYISSGSSTLHYA DTVKG RFTISRDN PKNTLFLQ Met KLPSLCYG LLGPRDHG HfSSGGGGSGGGGSGGGGSjELTQSPA SLAVSLGQRATISYRASKSVSTSGYSY Met H W NQQKPGQP PRLLIYLVS NLESGVPARFSGSG SGTDFTLNI HPVE EEDAATYYCQHI RELTRS E GAPSS
C10_VH4VK3 complete fMGDNDIHFAFLSTGVHSOVO! LQQSGGG LVQPG with IGk secretory GSRKLSCAASG FTFSSFG Met HWVRQAPEKG signal and c-myc LEWVAYISSGSSTLHYADTVKG RFTISRDN P peptide K N T L F L Q Met KLPS LCYG LLG PRDHG H{SSGGG
GSGGGGSGGGGSJELTQSPASLAVSLGQRATISY RASKSVSTSGYSY Met HWNQQKPGQPP RLLI YLVSN LESGVPARFSGSGSGTDFTLNI H PVE EEDAATYYCQHI RELTRS EGAPSSfEOKLISEE DLN]
C10_VH4VK3 full LQQSGGG LVQPG GSRKLSCAASG FTFSSF
G Met HWVRQAP EKG LEWVAYISSGSSTLHYA DTVKG RFTISRDN PKNTLFLQ Met KLPSLCYG LLG PRDHG H{SSGGGGSGGGGSGGGGS}ELTQSPA SLAVSLGQRATISYRASKSVSTSGYSY Met HW NQQKPGQP PRLLIYLVS NLESGVPARFSGSG SGTDFTLNI HPVE EEDAATYYCQHI RELTRS E GAPSS
TDP-43 MSEYIRVTED ENDEPIEIPS EDDGTVLLST VTAQFPGACG
LRYRNPVSQC MRGVRLVEGI LHAPDAGWGN LVYVVNYPKD NKRKMDETDA SSAVKVKRAV QKTSDLIVLG LPWKTTEQDL KEYFSTFGEV LMVQVKKDLK TGHSKGFGFV RFTEYETQVK VMSQRHMIDG RWCDCKLPNS KQSQDEPLRS RKVFVGRCTE DMTEDELREF FSQYGDVMDV FIPKPFRAFA FVTFADDQIA QSLCGEDLII KGISVHISNA EPKHNSNRQL ERSGRFGGNP GGFGNQGGFG NSRGGGAGLG NNQGSNMGGG MNFGAFSINP AMMAAAQAAL QSSWGMMGML ASQQNQSGPS GNNQNQGNMQ REPNQAFGSG NNSYSGSNSG AAIGWGSASN AGSGSGFNGG FGSSMDSKSS GWGM 0 NF-κΒ p65 MDELFPLIFPAEPAQASGPYVEIIEQPKQRGMRFRYKCEGRSAG
SIPGERSTDTTKTHPTIKINGYTGPGTVRISLVTKDPPHRPHPHELVGKDCRDGFYEA ELCPDRCIHSFQNLGIQCVKKRDLEQAISQRIQT NNPFQVPIEEQRGDYDLNAVRLC FQVTVRDPSGRPLRLPPVLPHPIFDNRAPNTAELKICRVNRNSGSCLGGDEIFLLCDK VQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPYADPSLQAPVRVSMQLRRPS DRELSEPMEFQYLPDTDDRHRIEEKRKRTYETFKSIMKKSPFSGPTDPRPPPRRIAVP SRSSASVPKPAPQPYPFTSSLSTINYDEFPTMVFPSGQISQASALAPAPPQVLPQAPA PAPAPAMVSALAQAPAPVPVLAPGPPQAVAPPAPKPTQAGEGTLSEALLQLQFDDEDL GALLGNSTDPAVFTDLASVDNSEFQQLLNQGIPVAPHTTEPMLMEYPEAITRLVTGAQ RPPDPAPAPLGAPGLPNGLLSGDEDFSSIADMDFSALLSQISS
Figure imgf000026_0001
TCAGGCTCCAGAGAAGGGGCTGGAGTGGGTCGCATACATTAGTAGTGGCAG TAGTACCCTCCACTATGCAGACACAGTGAAGGGCCGATTCACCATCTCCAGA GACAATCCCAAGAACACCCTGTTCCTGCAAATGAAACTACCCTCACTATGCT ATGGACTACTGGGGCCAAGGGACCACGGTCACC
C 10_VK3 light chain GAGCTCACCCAGTCTCCTGCTTCCTTAGCTGTATCTCTGGGGCAGAGGGCCA variable region CCATCTCATACAGGGCCAGCAAAAGTGTCAGTACATCTGGCTATAGTTATAT
GCACTGGAACCAACAGAAACCAGGACAGCCACCCAGACTCCTCATCTATCTT
GTATCCAACCTAGAATCTGGGGTCCCTGCCAGGTTCAGTGGCAGTGGGTCTG
GGACAGACTTCACCCTCAACATCCATCCTGTGGAGGAGGAGGATGCTGCAA
CCTATTACTGTCAGCACATTAGGGAGCTTACACGTTCGGAGGGGGCACCAAG
CTCGAG
E6_VH1VK9 clone atgggtgacaatgacatccactttgcctttctctccacaggtgtccactcccaggtccaCTGCAGG complete with Igk AGTCTGGAGGAGGCTTGGTGCAACCTGGAGGATCCATGAAACTCTCCTGTGT
TGCCTCTGGATTCACTTCCAGTAACTACTGGTTGAACTGGGTCCGCCAGTCTC
secretion signal and c-myc CAGAGAGGGGGCTTGAGTGGGTTGCTGAAATTAGATTGAAATCTAATAATTA peptide TGCAACAAATTATGCGGAGTCTGTGAAAGGGAGGTTCACCATCTCAAGAGA
CGATTCCAAAAGTAGTGTCTACCTGCAAGTGAACAACTTAAGAGCTGAAGA
CACTGGCATTTATTACTGTACCAGGTCAACAGCTCGGGCTACCCCATACTAC
TTTGACTACTGGGGCCAAGGGACCACGGTCACCGTCtCCtcaggtggaggCggttC aggcggaggtggctctggcggtggcggatcggacatcGAGCTCACCCAGTCTCCATCCT
CCCTGGCTGTGTCAGCCGGAGAGAAGGTCACTATGAGCTGCAAATCCAGTCA
GAGTCTGCTCAACAGTAGAGCCCGAAAGAACTTCTTGACTTGGTACCAGCAG
AAACCAGGGCAGTCTCCTAAATTGCTGATCTATTGGGCATCCACTAGGGAAT
CTGGGGTCCCTGATCGCTTCACAGGCAGTGGATCTGGGACAGATTTCACTCT
CACCATCAGCAGTGTGCAGGCTGAAGACCTGGCAGTTTATTACTGCAAACAG
TCTTATAATCTGTACACGTTCGGAGGGGGCACCAAGCTCGAGatcaaacgggaa caaaaactcatctcagaagaggatctgaat
E6 VH1 VK9 clone full CTGCAGGAGTCTGGAGGAGGCTTGGTGCAACCTGGAGGATCCATGAAACTC
TCCTGTGTTGCCTCTGGATTCACTTCCAGTAACTACTGGTTGAACTGGGTCCG
CCAGTCTCCAGAGAGGGGGCTTGAGTGGGTTGCTGAAATTAGATTGAAATCT
AATAATTATGCAACAAATTATGCGGAGTCTGTGAAAGGGAGGTTCACCATCT
CAAGAGACGATTCCAAAAGTAGTGTCTACCTGCAAGTGAACAACTTAAGAG
CTGAAGACACTGGCATTTATTACTGTACCAGGTCAACAGCTCGGGCTACCCC
ATACTACTTTGACTACTGGGGCCAAGGGACCACGGTCACCGTCtCCtcaggtgga ggcggttcaggcggaggtggctctggcggtggcggatcggacatcGAGCTCACCCAGTCT
CCATCCTCCCTGGCTGTGTCAGCCGGAGAGAAGGTCACTATGAGCTGCAAAT
CCAGTCAGAGTCTGCTCAACAGTAGAGCCCGAAAGAACTTCTTGACTTGGTA
CCAGCAGAAACCAGGGCAGTCTCCTAAATTGCTGATCTATTGGGCATCCACT
AGGGAATCTGGGGTCCCTGATCGCTTCACAGGCAGTGGATCTGGGACAGATT
TCACTCTCACCATCAGCAGTGTGCAGGCTGAAGACCTGGCAGTTTATTACTG
CAAACAGTCTTATAATCTGTACACGTTCGGAGGGGGCACCAAGCTCGAG
E6_VH7VK9 atgggtgacaatgacatccactttgcctttctctccacaggtgtccactcccaggtccaCTGCAGC clone complete with Igk AGTCTGGAGGAGGCTTGGTGCAACCTGGAGGATCCATGAAACTCTCCTGTGT
TGCCTCTGGATTCACTTCCAGTAACTACTGGTTGAACTGGGTCCGCCAGTCTC
secretion signal and c-myc CAGAGAGGGGGCTTGAGTGGGTTGCTGAAATTAGATTGAAATCTAATAATTA peptide TGCAACAAATTATGCGGAGTCTGTGAAAGGGAGGTTCACCATCTCAAGAGA
CGATTCCAAAAGTAGTGTCTACCTGCAAGTGAACAACTTAAGAGCTGAAGA
CACTGGCATTTATTACTGTACCAGGTCAACAGCTCGGGCTACCCCATACTAC TTTGACTACTGGGGCCAAGGGACCACGGTCACCTCtCCtcaggtggaggCggttca ggCggaggtggCtctggCggtggCggatCggacatcGAGCTCACCCAGTCTCCATCCTC
CCTGGCTGTGTCAGCCGGAGAGAAGGTCACTATGAGCTGCAAATCCAGTCA
GAGTCTGCTCAACAGTAGAGCCCGAAAGAACTTCTTGACTTGGTACCAGCAG
AAACCAGGGCAGTCTCCTAAATTGCTGATCTATTGGGCATCCACTAGGGAAT
CTGGGGTCCCTGATCGCTTCACAGGCAGTGGATCTGGGACAGATTTCACTCT
CACCATCAGCAGTGTGCAGGCTGAAGACCTGGCAGTTTATTACTGCAAACAG
TCTTATAATCTGTACACGTTCGGAGGGGGCACCAAGCTCGAGatcaaacgggaa caaaaactcatctcagaagaggatctgaat
E6_VH7VK9 clone full CTGCAGCAGTCTGGAGGAGGCTTGGTGCAACCTGGAGGATCCATGAAACTCT
CCTGTGTTGCCTCTGGATTCACTTCCAGTAACTACTGGTTGAACTGGGTCCGC
CAGTCTCCAGAGAGGGGGCTTGAGTGGGTTGCTGAAATTAGATTGAAATCTA
ATAATTATGCAACAAATTATGCGGAGTCTGTGAAAGGGAGGTTCACCATCTC
AAGAGACGATTCCAAAAGTAGTGTCTACCTGCAAGTGAACAACTTAAGAGC
TGAAGACACTGGCATTTATTACTGTACCAGGTCAACAGCTCGGGCTACCCCA
TACTACTTTGACTACTGGGGCCAAGGGACCACGGTCACCTCtCCtcaggtggagg cggttcaggcggaggtggctctggcggtggcggatcggacatcGAGCTCACCCAGTCTCC
ATCCTCCCTGGCTGTGTCAGCCGGAGAGAAGGTCACTATGAGCTGCAAATCC AGTCAGAGTCTGCTCAACAGTAGAGCCCGAAAGAACTTCTTGACTTGGTACC AGCAGAAACCAGGGCAGTCTCCTAAATTGCTGATCTATTGGGCATCCACTAG GGAATCTGGGGTCCCTGATCGCTTCACAGGCAGTGGATCTGGGACAGATTTC ACTCTCACCATCAGCAGTGTGCAGGCTGAAGACCTGGCAGTTTATTACTGCA AACAGTCTTATAATCTGTACACGTTCGGAGGGGGCACCAAGCTCGAG
C 10_VH3VK3 clone atgggtgacaatgacatccactttgcctttctctccacaggtgtccactcccaggtccaCTGCAGG complete with Igk AGTCTGGGGGAGGCTTAGTGCAGCCTGGAGGGTCCCGGAAACTCTCCTGTGC
AGCCTCTGGATTCACTTTCAGTAGCTTTGGAATGCACTGGGTTCGTCAGGCTC
secretion signal and c-myc CAGAGAAGGGGCTGGAGTGGGTCGCATACATTAGTAGTGGCAGTAGTACCC peptide TCCACTATGCAGACACAGTGAAGGGCCGATTCACCATCTCCAGAGACAATCC
CAAGAACACCCTGTTCCTGCAAATGAAACTACCCTCACTATGCTATGGACTA
CTGGGGCCAAGGGACCACGGTCACCtCCtcaggtggaggCggttcaggCggaggtggC tctggCggtggCggatCggacatcGAGCTCACCCAGTCTCCTGCTTCCTTAGCTGTAT
CTCTGGGGCAGAGGGCCACCATCTCATACAGGGCCAGCAAAAGTGTCAGTA
CATCTGGCTATAGTTATATGCACTGGAACCAACAGAAACCAGGACAGCCAC
CCAGACTCCTCATCTATCTTGTATCCAACCTAGAATCTGGGGTCCCTGCCAG
GTTCAGTGGCAGTGGGTCTGGGACAGACTTCACCCTCAACATCCATCCTGTG
GAGGAGGAGGATGCTGCAACCTATTACTGTCAGCACATTAGGGAGCTTACA
CGTTCGGAGGGGGCACCAAGCTCGAGatcaaacgggaacaaaaactcatctcagaaga ggatctgaat
C 10_VH3VK3 clone full CTGCAGGAGTCTGGGGGAGGCTTAGTGCAGCCTGGAGGGTCCCGGAAACTC
TCCTGTGCAGCCTCTGGATTCACTTTCAGTAGCTTTGGAATGCACTGGGTTCG
TCAGGCTCCAGAGAAGGGGCTGGAGTGGGTCGCATACATTAGTAGTGGCAG
TAGTACCCTCCACTATGCAGACACAGTGAAGGGCCGATTCACCATCTCCAGA
GACAATCCCAAGAACACCCTGTTCCTGCAAATGAAACTACCCTCACTATGCT
ATGGACTACTGGGGCCAAGGGACCACGGTCACCtCCtcaggtggaggCggttcagg
CggaggtggCtctggCggtggCggatCggacatcGAGCTCACCCAGTCTCCTGCTTCCT
TAGCTGTATCTCTGGGGCAGAGGGCCACCATCTCATACAGGGCCAGCAAAA
GTGTCAGTACATCTGGCTATAGTTATATGCACTGGAACCAACAGAAACCAGG
ACAGCCACCCAGACTCCTCATCTATCTTGTATCCAACCTAGAATCTGGGGTC
CCTGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACCCTCAACATCC
ATCCTGTGGAGGAGGAGGATGCTGCAACCTATTACTGTCAGCACATTAGGGA
GCTTACACGTTCGGAGGGGGCACCAAGCTCGAG
C 10_VH4VK3 clone atgggtgacaatgacatccactttgcctttctctccacaggtgtccactcccaggtccaCTGCAGC complete with Igk AGTCAGGGGGAGGCTTAGTGCAGCCTGGAGGGTCCCGGAAACTCTCCTGTG
CAGCCTCTGGATTCACTTTCAGTAGCTTTGGAATGCACTGGGTTCGTCAGGCT secretion signal and c-myc CCAGAGAAGGGGCTGGAGTGGGTCGCATACATTAGTAGTGGCAGTAGTACC peptide CTCCACTATGCAGACACAGTGAAGGGCCGATTCACCATCTCCAGAGACAATC
CCAAGAACACCCTGTTCCTGCAAATGAAACTACCCTCACTATGCTATGGACT
ACTGGGGCCAAGGGACCACGGTCACCtCCtcaggtggaggCggttcaggCggaggtg gCtctggCggtggCggatCggacatcGAGCTCACCCAGTCTCCTGCTTCCTTAGCTGT
ATCTCTGGGGCAGAGGGCCACCATCTCATACAGGGCCAGCAAAAGTGTCAG
TACATCTGGCTATAGTTATATGCACTGGAACCAACAGAAACCAGGACAGCC
ACCCAGACTCCTCATCTATCTTGTATCCAACCTAGAATCTGGGGTCCCTGCCA
GGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACCCTCAACATCCATCCTGT
GGAGGAGGAGGATGCTGCAACCTATTACTGTCAGCACATTAGGGAGCTTAC
ACGTTCGGAGGGGGCACCAAGCTCGAGatcaaacgggaacaaaaactcatctcagaag aggatctgaat
C 10_VH4VK3 clone full CTGCAGCAGTCAGGGGGAGGCTTAGTGCAGCCTGGAGGGTCCCGGAAACTC
TCCTGTGCAGCCTCTGGATTCACTTTCAGTAGCTTTGGAATGCACTGGGTTCG
TCAGGCTCCAGAGAAGGGGCTGGAGTGGGTCGCATACATTAGTAGTGGCAG
TAGTACCCTCCACTATGCAGACACAGTGAAGGGCCGATTCACCATCTCCAGA
GACAATCCCAAGAACACCCTGTTCCTGCAAATGAAACTACCCTCACTATGCT
ATGGACTACTGGGGCCAAGGGACCACGGTCACCtCCtcaggtggaggCggttcagg
CggaggtggCtctggCggtggCggatCggacatcGAGCTCACCCAGTCTCCTGCTTCCT
TAGCTGTATCTCTGGGGCAGAGGGCCACCATCTCATACAGGGCCAGCAAAA
GTGTCAGTACATCTGGCTATAGTTATATGCACTGGAACCAACAGAAACCAGG
ACAGCCACCCAGACTCCTCATCTATCTTGTATCCAACCTAGAATCTGGGGTC
CCTGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACCCTCAACATCC
ATCCTGTGGAGGAGGAGGATGCTGCAACCTATTACTGTCAGCACATTAGGGA
GCTTACACGTTCGGAGGGGGCACCAAGCTCGAG
Linker signal SSGGGGSGGGGSGGGGS
Secretory signal MGDNDIHFAFLSTGVHSQVQ
Polypeptides and polynucleotides
[0084] The antigen-binding constructs described herein comprise at least one TDP-43- binding polypeptide. Also described are polynucleotides encoding the TDP-43 -binding polypeptides described herein.
[0085] As used herein, "isolated" means an agent (e.g., a polypeptide or polynucleotide) that has been identified and separated and/or recovered from a component of its natural cell culture environment. Contaminant components of its natural environment are materials that would interfere with diagnostic or therapeutic uses for the antigen-binding construct, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. Isolated also refers to an agent that has been synthetically produced, e.g., via human intervention. [0086] The terms "polypeptide," "peptide" and "protein" are used interchangeably herein to refer to a polymer of amino acid residues. That is, a description directed to a polypeptide applies equally to a description of a peptide and a description of a protein, and vice versa. The terms apply to naturally occurring amino acid polymers as well as amino acid polymers in which one or more amino acid residues is a non-naturally encoded amino acid. As used herein, the terms encompass amino acid chains of any length, including full length proteins, wherein the amino acid residues are linked by covalent peptide bonds.
[0087] The term "amino acid" refers to naturally occurring and non-naturally occurring amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally encoded amino acids are the 20 common amino acids (alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, praline, serine, threonine, tryptophan, tyrosine, and valine) and pyrrolysine and selenocysteine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, such as, homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (such as, norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Reference to an amino acid includes, for example, naturally occurring proteogenic L-amino acids; D-amino acids, chemically modified amino acids such as amino acid variants and derivatives; naturally occurring non -proteogenic amino acids such as β-alanine, ornithine, etc.; and chemically synthesized compounds having properties known in the art to be characteristic of amino acids. Examples of non-naturally occurring amino acids include, but are not limited to, oc- methyl amino acids (e.g. oc-methyl alanine), D-amino acids, histidine-like amino acids (e.g., 2-amino-histidine, β-hydroxy-histidine, homohistidine), amino acids having an extra methylene in the side chain ("homo" amino acids), and amino acids in which a carboxylic acid functional group in the side chain is replaced with a sulfonic acid group (e.g., cysteic acid). The incorporation of non-natural amino acids, including synthetic non-native amino acids, substituted amino acids, or one or more D-amino acids into the proteins as described herein may be advantageous in a number of different ways. D-amino acid-containing peptides, etc., exhibit increased stability in vitro or in vivo compared to L-amino acid- containing counterparts. Thus, the construction of peptides, etc., incorporating D-amino acids can be particularly useful when greater intracellular stability is desired or required. More specifically, D-peptides, etc., are resistant to endogenous peptidases and proteases, thereby providing improved bioavailability of the molecule, and prolonged lifetimes in vivo when such properties are desirable. Additionally, D-peptides, etc., cannot be processed efficiently for major histocompatibility complex class II-restricted presentation to T helper cells, and are therefore, less likely to induce humoral immune responses in the whole organism.
[0088] Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
[0089] Also included are polynucleotides encoding polypeptides of the antigen-binding constructs. The term "polynucleotide" or "nucleotide sequence" is intended to indicate a consecutive stretch of two or more nucleotide molecules. The nucleotide sequence may be of genomic, cDNA, RNA, semisynthetic or synthetic origin, or any combination thereof. [0090] The term "nucleic acid" refers to deoxyribonucleotides, deoxyribonucleosides, ribonucleosides, or ribonucleotides and polymers thereof in either single- or double- stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides which have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless specifically limited otherwise, the term also refers to oligonucleotide analogs including PNA (peptidonucleic acid), analogs of DNA used in antisense technology (phosphorothioates, phosphoroamidates, and the like). Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (including but not limited to, degenerate codon substitutions) and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)).
[0091] "Conservatively modified variants" applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, "conservatively modified variants" refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are "silent variations," which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of ordinary skill in the art will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.
[0092] As to amino acid sequences, one of ordinary skill in the art will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the deletion of an amino acid, addition of an amino acid, or substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are known to those of ordinary skill in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles as described herein.
[0093] Conservative substitution tables providing functionally similar amino acids are known to those of ordinary skill in the art. The following eight groups each contain amino acids that are conservative substitutions for one another: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and [0139] 8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins: Structures and Molecular Properties (W H Freeman & Co.; 2nd edition (December 1993).
[0094] The terms "identical" or percent "identity," in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same. Sequences are "substantially identical" if they have a percentage of amino acid residues or nucleotides that are the same (i.e., about 60% identity, about 65%, about 70%, about 75%), about 80%>, about 85%, about 90%, or about 95% identity over a specified region), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms (or other algorithms available to persons of ordinary skill in the art) or by manual alignment and visual inspection. This definition also refers to the complement of a test sequence. The identity can exist over a region that is at least about 50 amino acids or nucleotides in length, or over a region that is 75-100 amino acids or nucleotides in length, or, where not specified, across the entire sequence of a polynucleotide or polypeptide. A polynucleotide encoding a polypeptide as described herein, including homologs from species other than human, may be obtained by a process comprising the steps of screening a library under stringent hybridization conditions with a labeled probe having a polynucleotide sequence as described herein or a fragment thereof, and isolating full-length cDNA and genomic clones containing said polynucleotide sequence. Such hybridization techniques are well known to the skilled artisan. [0095] For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
[0096] A "comparison window", as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are known to those of ordinary skill in the art. Optimal alignment of sequences for comparison can be conducted, including but not limited to, by the local homology algorithm of Smith and Waterman (1970) Adv. Appl. Math. 2:482c, by the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity method of Pearson and Lipman (1988) Proc. Nat'l. Acad. Sci. USA 85:2444, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Ausubel et al., Current Protocols in Molecular Biology (1995 supplement)).
[0097] One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1997) Nuc. Acids Res. 25:3389-3402, and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information available at the World Wide Web at ncbi.nlm.nih.gov. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) or 10, M=5, N=-4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1992) Proc. Natl. Acad. Sci. USA 89: 10915) alignments (B) of 50, expectation (E) of 10, M=5, N=-4, and a comparison of both strands. The BLAST algorithm is typically performed with the "low complexity" filter turned off.
[0098] The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873- 5787). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, or less than about 0.01, or less than about 0.001.
[0099] The phrase "selectively (or specifically) hybridizes to" refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (including but not limited to, total cellular or library DNA or RNA).
[00100] The phrase "stringent hybridization conditions" refers to hybridization of sequences of DNA, RNA, or other nucleic acids, or combinations thereof under conditions of low ionic strength and high temperature as is known in the art. Typically, under stringent conditions a probe will hybridize to its target subsequence in a complex mixture of nucleic acid (including but not limited to, total cellular or library DNA or RNA) but does not hybridize to other sequences in the complex mixture. Stringent conditions are sequence- dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Laboratory Techniques in Biochemistry and Molecular Biology- Hybridization with Nucleic Probes, "Overview of principles of hybridization and the strategy of nucleic acid assays" (1993). [00101] As used herein, the terms "engineer, engineered, engineering", are considered to include any manipulation of the peptide backbone or the post-translational modifications of a naturally occurring or recombinant polypeptide or fragment thereof. Engineering includes modifications of the amino acid sequence, of the glycosylation pattern, or of the side chain group of individual amino acids, as well as combinations of these approaches. The engineered proteins are expressed and produced by standard molecular biology techniques.
[00102] By "isolated nucleic acid molecule or polynucleotide" is intended a nucleic acid molecule, DNA or RNA, which has been removed from its native environment. For example, a recombinant polynucleotide encoding a polypeptide contained in a vector is considered isolated. Further examples of an isolated polynucleotide include recombinant polynucleotides maintained in heterologous host cells or purified (partially or substantially) polynucleotides in solution. An isolated polynucleotide includes a polynucleotide molecule contained in cells that ordinarily contain the polynucleotide molecule, but the polynucleotide molecule is present extrachromosomally or at a chromosomal location that is different from its natural chromosomal location. Isolated RNA molecules include in vivo or in vitro RNA transcripts, as well as positive and negative strand forms, and double- stranded forms. Isolated polynucleotides or nucleic acids described herein, further include such molecules produced synthetically, e.g., via PCR or chemical synthesis. In addition, a polynucleotide or a nucleic acid, in certain embodiments, include a regulatory element such as a promoter, ribosome binding site, or a transcription terminator.
[00103] The term "polymerase chain reaction" or "PCR" generally refers to a method for amplification of a desired nucleotide sequence in vitro, as described, for example, in U.S. Pat. No. 4,683, 195. In general, the PCR method involves repeated cycles of primer extension synthesis, using oligonucleotide primers capable of hybridising preferentially to a template nucleic acid.
[00104] By a nucleic acid or polynucleotide having a nucleotide sequence at least, for example, 95% "identical" to a reference nucleotide sequence as described herein, it is intended that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence. In other words, to obtain a polynucleotide having a nucleotide sequence at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. These alterations of the reference sequence may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence. As a practical matter, whether any particular polynucleotide sequence is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a nucleotide sequence as described herein can be determined conventionally using known computer programs, such as the ones discussed above for polypeptides (e.g. ALIGN-2). [00105] A derivative, or a variant of a polypeptide is said to share "homology" or be "homologous" with the peptide if the amino acid sequences of the derivative or variant has at least 50% identity with a 100 amino acid sequence from the original peptide. In certain embodiments, the derivative or variant is at least 75% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In certain embodiments, the derivative or variant is at least 85% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In certain embodiments, the amino acid sequence of the derivative is at least 90% the same as the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In some embodiments, the amino acid sequence of the derivative is at least 95% the same as the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In certain embodiments, the derivative or variant is at least 99% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. [00106] The term "modified," as used herein refers to any changes made to a given polypeptide, such as changes to the length of the polypeptide, the amino acid sequence, chemical structure, co-translational modification, or post-translational modification of a polypeptide. The form "(modified)" term means that the polypeptides being discussed are optionally modified, that is, the polypeptides under discussion can be modified or unmodified.
[00107] In some aspects, an antigen-binding construct comprises an amino acids sequence that is at least 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identical to a relevant amino acid sequence or fragment thereof set forth in the Table(s) or accession number(s) disclosed herein. In some aspects, an isolated antigen-binding construct comprises an amino acids sequence encoded by a polynucleotide that is at least 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identical to a relevant nucleotide sequence or fragment thereof set forth in Table(s) or accession number(s) disclosed herein.
[00108] In certain embodiments the antigen-binding polypeptide is derived from humanized, or chimeric versions of these antibodies.
[00109] "Humanized" forms of non-human (e.g., rodent) antibodies are chimeric antibodies that contain minimal sequence derived from non-human immunoglobulin. For the most part, humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and capacity. In some instances, framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non- human immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence. The humanized antibody optionally also may comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details, see Jones et al., Nature 321 :522-525 (1986); Riechmann et al., Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593- 596 (1992). In some embodiments, the anti-TDP-43 antigen binding constructs are humanized. In one embodiment, the humanized anti-TDP-43 antibodies comprise the amino acids of murine CDRs.
[00110] De-immunization can also be used to decrease the immunogemcity of an antibody.
[00111] As used herein, the term "de-immunization" includes alteration of an antibody to modify T cell epitopes; see, e.g., international Application Publication Nos. W098/52976 and WO00/34317. For example, VH and VL sequences from the starting antibody are analyzed and a human T cell epitope "map" from each V region showing the location of epitopes in relation to complementarity determining regions (CDRs) and other key residues within the sequence. Individual T cell epitopes from the T cell epitope map are analyzed in order to identify alternative amino acid substitutions with a low risk of altering activity of the final antibody. A range of alternative VH and VL sequences are designed comprising combinations of amino acid substitutions and these sequences are subsequently incorporated into a range of binding polypeptides, e.g., TDP-43 -specific antibodies, including immunospecific fragments thereof, for use in the diagnostic and treatment methods disclosed herein, which are then tested for function. Typically, between 12 and 24 variant antibodies are generated and tested. Complete heavy and light chain genes comprising modified V and/or C regions are then cloned into expression vectors and the subsequent plasmids introduced into cell lines for the production of whole antibody. The antibodies are then compared in appropriate biochemical and biological assays, and the optimal variant is identified. Pharmaceutical compositions
[00112] Also provided herein are pharmaceutical compositions comprising an antigen- binding constructs described herein. Such compositions comprise the construct and a pharmaceutically acceptable carrier. [00113] The term "pharmaceutically acceptable" means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. The term "carrier" refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. In some aspects, the carrier is a man-made carrier not found in nature. Water can be used as a carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical carriers are described in "Remington's Pharmaceutical Sciences" by E. W. Martin. Such compositions will contain a therapeutically effective amount of the compound, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. The formulation should suit the mode of administration. [00114] In certain embodiments, the composition comprising the construct is formulated in accordance with routine procedures as a pharmaceutical composition adapted for intravenous administration to human beings. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the composition is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.
[00115] In certain embodiments, the compositions described herein are formulated as neutral or salt forms. Pharmaceutically acceptable salts include those formed with anions such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with cations such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxide isopropyl amine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc. Methods of preparation of TDP-43 antigen-binding constructs
[00116] Also described herein are methods of producing the anti-TDP-43 antigen- binding constructs. In certain embodiments the antigen-binding constructs are produced as recombinant molecules by expression in a cell, e.g., yeast, a microorganism such as a bacterium, or a human or animal cell line. In embodiments, the anti-TDP-43 antigen- binding constructs are secreted from the cells.
[00117] The antigen-binding constructs can be expressed in a host cell using an expression cassette coding for the antigen-binding construct. The term "expression cassette" refers to a polynucleotide generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a target cell. The recombinant expression cassette can be incorporated into a vector, e.g., a plasmid, chromosome, mitochondrial DNA, plastid DNA, virus, or nucleic acid fragment. Typically, the recombinant expression cassette portion of an expression vector includes, among other sequences, a nucleic acid sequence to be transcribed and a promoter. In certain embodiments, the expression cassette as described herein comprises polynucleotide sequences that encode antigen-binding constructs as described herein or fragments thereof.
[00118] The term "vector" or "expression vector" is synonymous with "expression construct" and refers to a nucleic acid molecule that is used to introduce and direct the expression of a specific gene to which it is operably associated in a target cell. The term includes the vector as a self-replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which it has been introduced. The expression vector as described herein comprises an expression cassette. Expression vectors allow transcription of large amounts of stable mRNA. Once the expression vector is inside the target cell, the ribonucleic acid molecule or protein that is encoded by the gene is produced by the cellular transcription and/or translation machinery. In one embodiment, the expression vector as described herein comprises an expression cassette that comprises polynucleotide sequences that encode antigen-binding constructs as described herein or fragments thereof. Exemplary vectors are described herein. [00119] Typically a host cell is transformed with an expression vector coding for an antigen-binding construct. "Cell", "host cell", "cell line" and "cell culture" are used interchangeably herein and all such terms should be understood to include progeny resulting from growth or culturing of a cell. "Transformation" and "transfection" are used interchangeably to refer to the process of introducing DNA into a cell. . Host cells include "transformants" and "transformed cells," which include the primary transformed cell and progeny derived therefrom without regard to the number of passages. In certain embodiments, progeny are not completely identical in nucleic acid content to a parent cell, but may contain mutations. Mutant progeny that have the same function or biological activity as screened or selected for in the originally transformed cell are included herein. [00120] A host cell is any type of cellular system that can be used to generate the antigen-binding constructs as described herein. Host cells include cultured cells, e.g. mammalian cultured cells, such as CHO cells, BHK cells, NS0 cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells or hybridoma cells, bacteria (for example E. coli and Bacillus subtilis), yeasts (for example Saccharomyces cerevisiae, Kluyveromyces lactis and Pichia pastoris, filamentous fungi (for example Aspergillus), insect cells, and plant cells, to name only a few, but also cells comprised within a transgenic animal, transgenic plant or cultured plant or animal tissue. Additional examples of host cells are described herein. [00121] In some embodiments, the antigen-binding construct is produced in a mammalian cell. In select embodiments, the mammalian cell is selected from the group consisting of a VERO, HeLa, HEK, NS0, Chinese Hamster Ovary (CHO), W138, BHK, COS-7, Caco-2 and MDCK cell, and subclasses and variants thereof.
Expression vectors
[00122] Provided are vectors containing polynucleotides encoding an antigen- binding construct described herein, host cells, and the production of the antigen-binding construct proteins by synthetic and recombinant techniques. The vector may be, for example, a phage, plasmid, viral, or retroviral vector. Retroviral vectors may be replication competent or replication defective. In the latter case, viral propagation generally will occur only in complementing host cells.
[00123] In certain embodiments, the polynucleotides encoding antigen-binding construct proteins described herein are joined to a vector containing a selectable marker for propagation in a host. Generally, a plasmid vector is introduced in a precipitate, such as a calcium phosphate precipitate, or in a complex with a charged lipid. If the vector is a virus, it may be packaged in vitro using an appropriate packaging cell line and then transduced into host cells.
[00124] In certain embodiments, the polynucleotide insert is operatively linked to an appropriate promoter, such as the phage lambda PL promoter, the E. coli lac, trp, phoA and rac promoters, the SV40 early and late promoters and promoters of retroviral LTRs, to name a few. Other suitable promoters will be known to the skilled artisan. The expression constructs will further contain sites for transcription initiation, termination, and, in the transcribed region, a ribosome binding site for translation. The coding portion of the transcripts expressed by the constructs will preferably include a translation initiating codon at the beginning and a termination codon (UAA, UGA or UAG) appropriately positioned at the end of the polypeptide to be translated.
[00125] As indicated, the expression vectors will preferably include at least one selectable marker. Such markers include dihydrofolate reductase, G418, glutamine synthase, or neomycin resistance for eukaryotic cell culture, and tetracycline, kanamycin or ampicillin resistance genes for culturing in E. coli and other bacteria. Representative examples of appropriate hosts include, but are not limited to, bacterial cells, such as E. coli, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells (e.g., Saccharomyces cerevisiae or Pichia pastoris (ATCC Accession No. 201178)); insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, NSO, 293, and Bowes melanoma cells; and plant cells. Appropriate culture mediums and conditions for the above-described host cells are known in the art.
[00126] Among vectors preferred for use in bacteria include pQE70, pQE60 and pQE-9, available from QIAGEN, Inc.; pBluescript vectors, Phagescript vectors, pNH8A, pNH16a, pNH18A; pNH46A, available from Stratagene Cloning Systems, Inc.; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 available from Pharmacia Biotech, Inc.
Among preferred eukaryotic vectors are pWLNEO, pSV2CAT, pOG44, pXTl and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL available from Pharmacia.
Preferred expression vectors for use in yeast systems include, but are not limited to pYES2, pYDl, pTEFl/Zeo, pYES2/GS, pPICZ, pGAPZ, pGAPZalph, pPIC9, pPIC3.5, pHIL-D2, pHIL-Sl, pPIC3.5K, pPIC9K, and PA0815 (all available from Invitrogen, Carlsbad, CA).
Other suitable vectors will be readily apparent to the skilled artisan.
[00127] In one embodiment, polynucleotides encoding an antigen-binding construct described herein are fused to signal sequences that will direct the localization of a protein as described herein to particular compartments of a prokaryotic or eukaryotic cell and/or direct the secretion of a protein as described herein from a prokaryotic or eukaryotic cell. For example, in E. coli, one may wish to direct the expression of the protein to the periplasmic space. Examples of signal sequences or proteins (or fragments thereof) to which the antigen-binding construct proteins are fused in order to direct the expression of the polypeptide to the periplasmic space of bacteria include, but are not limited to, the pelB signal sequence, the maltose binding protein (MBP) signal sequence, MBP, the ompA signal sequence, the signal sequence of the periplasmic E. coli heat-labile enterotoxin B- subunit, and the signal sequence of alkaline phosphatase. Several vectors are commercially available for the construction of fusion proteins which will direct the localization of a protein, such as the pMAL series of vectors (particularly the pMAL-.rho. series) available from New England Biolabs. In a specific embodiment, polynucleotides encoding proteins as described herein may be fused to the pelB pectate lyase signal sequence to increase the efficiency of expression and purification of such polypeptides in Gram-negative bacteria. See, U.S. Pat. Nos. 5,576, 195 and 5,846,818, the contents of which are herein incorporated by reference in their entireties.
[00128] Examples of signal peptides that are fused to an antigen-binding construct protein in order to direct its secretion in mammalian cells include, but are not limited to, the MPIF-1 signal sequence (e.g., amino acids 1-21 of GenBank Accession number AAB51134), the stanniocalcin signal sequence (MLQNSAVLLLLVISASA (SEQ ID NO: 51)), and a consensus signal sequence (MPTWAWWLFLVLLLALWAPARG(SEQ ID NO: 52)). A suitable signal sequence that may be used in conjunction with baculoviral expression systems is the gp67 signal sequence (e.g., amino acids 1-19 of GenBank Accession Number AAA72759). In one embodiment, the signal sequence is an IgK secretory signal comprising the amino acid sequence (M G D N D I H F A F L S T G V H S Q V Q (SEQ ID NO: 53)). In one embodiment the IgK secretory signal is fused to the N- terminal of an TDP-43- binding polypeptide.
[00129] Vectors which use glutamine synthase (GS) or DHFR as the selectable markers can be amplified in the presence of the drugs methionine sulphoximine or methotrexate, respectively. An advantage of glutamine synthase based vectors are the availability of cell lines (e.g., the murine myeloma cell line, NSO) which are glutamine synthase negative. Glutamine synthase expression systems can also function in glutamine synthase expressing cells (e.g., Chinese Hamster Ovary (CHO) cells) by providing additional inhibitor to prevent the functioning of the endogenous gene. A glutamine synthase expression system and components thereof are detailed in PCT publications: WO87/04462; WO86/05807; WO89/10036; WO89/10404; and WO91/06657, which are hereby incorporated in their entireties by reference herein. Additionally, glutamine synthase expression vectors can be obtained from Lonza Biologies, Inc. (Portsmouth, N.H.). Expression and production of monoclonal antibodies or antigen-binding constructs using a GS expression system in murine myeloma cells is described in Bebbington et al., Bio/technology 10: 169(1992) and in Biblia and Robinson Biotechnol. Prog. 11 : 1(1995) which are herein incorporated by reference.
Host cells
[00130] Also provided are host cells containing vector constructs described herein, and additionally host cells containing nucleotide sequences that are operably associated with one or more heterologous control regions (e.g., promoter and/or enhancer) using techniques known of in the art. The host cell can be a higher eukaryotic cell, such as a mammalian cell (e.g., a human derived cell), or a lower eukaryotic cell, such as a yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial cell. A host strain may be chosen which modulates the expression of the inserted gene sequences, or modifies and processes the gene product in the specific fashion desired. Expression from certain promoters can be elevated in the presence of certain inducers; thus expression of the genetically engineered polypeptide may be controlled. Furthermore, different host cells have characteristics and specific mechanisms for the translational and post-translational processing and modification (e.g., phosphorylation, cleavage) of proteins. Appropriate cell lines can be chosen to ensure the desired modifications and processing of the foreign protein expressed. [00131] Mammalian cell lines available as hosts for expression are well known in the art and include many immortalized cell lines available from the American Type Culture Collection (ATCC), including but not limited to Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (e.g., Hep G2), human epithelial kidney 293 cells, and a number of other cell lines. Cell lines of particular preference are selected through determining which cell lines have high expression levels and produce antibodies with constitutive ManLAM binding properties.
[00132] Introduction of the nucleic acids and nucleic acid constructs as described herein into the host cell can be effected by calcium phosphate transfection; DEAE-dextran mediated transfection, cationic lipid-mediated transfection, electroporation, transduction, infection, or other methods. Such methods are described in many standard laboratory manuals, such as Davis et al., Basic Methods In Molecular Biology (1986). It is specifically contemplated that the polypeptides as described herein may in fact be expressed by a host cell lacking a recombinant vector.
[00133] In addition to encompassing host cells containing the vector constructs discussed herein, one embodiment also encompasses primary, secondary, and immortalized host cells of vertebrate origin, particularly mammalian origin, that have been engineered to delete or replace endogenous genetic material (e.g., the coding sequence corresponding to a Cargo polypeptide is replaced with an antigen-binding construct protein corresponding to the Cargo polypeptide), and/or to include genetic material. The genetic material operably associated with the endogenous polynucleotide may activate, alter, and/or amplify endogenous polynucleotides.
[00134] In addition, techniques known in the art may be used to operably associate heterologous polynucleotides (e.g., polynucleotides encoding a protein, or a fragment or variant thereof) and/or heterologous control regions (e.g., promoter and/or enhancer) with endogenous polynucleotide sequences encoding a therapeutic protein via homologous recombination (see, e.g., U.S. Pat. No. 5,641,670, issued Jun. 24, 1997; International Publication Number WO 96/29411; International Publication Number WO 94/12650; Roller et al., Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); and Zijlstra et al., Nature 342:435-438 (1989), the disclosures of each of which are incorporated by reference in their entireties).
Purification
[00135] Antigen-binding construct proteins described herein can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography such as with protein A, hydroxyl apatite chromatography, hydrophobic charge interaction chromatography and lectin chromatography. Most preferably, high performance liquid chromatography ("HPLC") is employed for purification.
[00136] In certain embodiments the antigen-binding construct proteins as described herein are purified using Anion Exchange Chromatography including, but not limited to, chromatography on Q-sepharose, DEAE sepharose, poros HQ, poros DEAF, Toyopearl Q, Toyopearl QAE, Toyopearl DEAE, Resource/Source Q and DEAE, Fractogel Q and DEAE columns.
[00137] In certain embodiments the proteins described herein may be purified using
Cation Exchange Chromatography including, but not limited to, SP-sepharose, CM sepharose, poros HS, poros CM, Toyopearl SP, Toyopearl CM, Resource/Source S and CM, Fractogel S and CM columns and their equivalents and comparables.
Chemical synthesis and cell-free expression
[00138] In addition, antigen-binding construct proteins described herein can be chemically synthesized using techniques known in the art (e.g., see Creighton, 1983, Proteins: Structures and Molecular Principles, W. H. Freeman & Co., N.Y and Hunkapiller et al., Nature, 310: 105-111 (1984)). For example, a polypeptide corresponding to a fragment of a polypeptide can be synthesized by use of a peptide synthesizer. Furthermore, if desired, nonclassical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the polypeptide sequence. Non-classical amino acids include, but are not limited to, to the D-isomers of the common amino acids, 2,4diaminobutyric acid, alpha-amino isobutyric acid, 4aminobutyric acid, Abu, 2-amino butyric acid, g-Abu, e-Ahx, 6amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, β-alanine, fluoro-amino acids, designer amino acids such as β-methyl amino acids, Coc-methyl amino acids, Na-methyl amino acids, and amino acid analogs in general. Furthermore, the amino acid can be D (dextrorotary) or L (levorotary). [00139] In certain embodiments, cell-free protein expression systems are utilized to co- express polypeptides (e.g., heavy and light chain polypeptides) without the use of living cells. Instead, all components needed to transcribe DNA to RNA and translate the RNA to protein (e.g. ribosomes, tRNAs, enzymes, cofactors, amino acids) are provided in solution for use in vitro. In certain embodiments, the in vitro expression requires (1) the genetic template (mRNA or DNA) encoding the heavy and light chain polypeptides and (2) a reaction solution containing the necessary transcriptional and translational molecular machinery. In certain embodiments, cell extracts substantially supply components of the reaction solution, for instance: RNA polymerases for mRNA transcription, ribosomes for polypeptide translation, tRNA, amino acids, enzymatic cofactors, an energy source, and cellular components essential for proper protein folding. Cell-free protein expression systems can be prepared using lysates derived from bacterial cells, yeast cells, insect cells, plant cells, mammalian cells, human cells or combinations thereof. Such cell lysates can provide the correct composition and proportion of enzymes and building blocks required for translation. In some embodiments, cell membranes are removed to leave only the cytosolic and organelle components of the cell.
[00140] Several cell-free protein expression systems are known in the art as reviewed in Carlson et al. (2012) Biotechnol. Adv. 30: 1185-1194. For example, cell-free protein expression systems are available based on prokaryotic or eukaryotic cells. Examples of prokaryotic cell-free expression systems include those from E. coli. Eukaryotic cell-free protein expression systems are available based on extracts from rabbit reticulocytes, wheat germ, and insect cells, for example. Such prokaryotic and eukaryotic cell-free protein expression systems are commercially available from companies such as Roche, Invitrogen, Qiagen, and Novagen. One skilled in the art would readily be able to select suitable cell- free protein expression systems that would produce polypeptides (e.g., heavy chain and light chain polypeptides) that are capable of pairing with each other. Further, the cell-free protein expression system can also be supplemented with chaperones (e.g. BiP) and isomerases (e.g. disulphide isomerase) to improve the efficiency of IgG folding.
[00141] In some embodiments, cell-free expression systems are utilized to co- express the heavy and light chain polypeptides from DNA templates (transcription and translation) or mRNA templates (translation only).
Expression in yeast
[00142] In some embodiments, the antigen-binding construct is produced in a yeast cell. The yeasts are transformed with a coding sequence for the desired protein in any of the usual ways, for example electroporation. Methods for transformation of yeast by electroporation are disclosed in Becker & Guarente (1990) Methods Enzymol. 194, 182.
[00143] Useful yeast plasmid vectors include pRS403-406 and pRS413-416 and are generally available from Stratagene Cloning Systems, La Jolla, Calif. 92037, USA. Plasmids pRS403, pRS404, pRS405 and pRS406 are Yeast Integrating plasmids (Yips) and incorporate the yeast selectable markers HIS3, 7RP1, LEU2 and URA3. Plasmids pRS413- 416 are Yeast Centromere plasmids (Ycps).
[00144] Exemplary genera of yeast contemplated to be useful in one embodimentas hosts for expressing the proteins are Pichua (formerly classified as Hansenula), Saccharomyces, Kluyveromyces, Aspergillus, Candida, Torulopsis, Torulaspora, Schizosaccharomyces, Citeromyces, Pachysolen, Zygosaccharomyces, Debaromyces, Trichoderma, Cephalosporium, Humicola, Mucor, Neurospora, Yarrowia, Metschunikowia, Rhodosporidium, Leucosporidium, Botryoascus, Sporidiobolus, Endomycopsis, and the like. Preferred genera are those selected from the group consisting of Saccharomyces, Schizosaccharomyces, Kluyveromyces, Pichia and Torulaspora. Examples of Saccharomyces spp. are S. cerevisiae, S. italicus and S. rouxii.
[00145] Examples of Kluyveromyces spp. are K. fragilis, K. lactis and K. marxianus.
A suitable Torulaspora species is T. delbrueckii. Examples of Pichia (Hansenula) spp. are P. angusta (formerly H. polymorpha), P. anomala (formerly H. anomala) and P. pastoris. Methods for the transformation of S. cerevisiae are taught generally in EP 251 744, EP 258 067 and WO 90/01063, all of which are incorporated herein by reference.
[00146] Exemplary species of Saccharomyces useful for the synthesis of antigen- binding constructs described herein include S. cerevisiae, S. italicus, S. diastaticus, and Zygosaccharomyces rouxii. Preferred exemplary species of Kluyveromyces include K. fragilis and K. lactis. Preferred exemplary species of Hansenula include H. polymorpha (now Pichia angusta), H. anomala (now Pichia anomala), and Pichia capsulata. Additional preferred exemplary species of Pichia include P. pastoris. Preferred exemplary species of Aspergillusinclude A. niger and A. nidulans. Preferred exemplary species of Yarrowia include Y. lipolytica. Many preferred yeast species are available from the ATCC. For example, the following preferred yeast species are available from the ATCC and are useful in the expression of proteins: Saccharomyces cerevisiae, Hansen, teleomorph strain BY4743 yap3 mutant (ATCC Accession No. 4022731); Saccharomyces cerevisiae Hansen, teleomorph strain BY4743 hspl50 mutant (ATCC Accession No. 4021266); Saccharomyces cerevisiae Hansen, teleomorph strain BY4743 pmtl mutant (ATCC Accession No. 4023792); Saccharomyces cerevisiae Hansen, teleomorph (ATCC Accession Nos. 20626; 44773; 44774; and 62995); Saccharomyces diastaticus Andrews et Gilliland ex van der Walt, teleomorph (ATCC Accession No. 62987); Kluyveromyces lactis (Dombrowski) van der Walt, teleomorph (ATCC Accession No. 76492); Pichia angusta (Teunisson et al.) Kurtzman, teleomorph deposited as Hansenula polymorpha de Morais et Maia, teleomorph (ATCC Accession No. 26012); Aspergillus niger van Tieghem, anamorph (ATCC Accession No. 9029); Aspergillus niger van Tieghem, anamorph (ATCC Accession No. 16404); Aspergillus nidulans (Eidam) Winter, anamorph (ATCC Accession No. 48756); and Yarrowia lipolytica (Wickerham et al.) van der Walt et von Arx, teleomorph (ATCC Accession No. 201847).
[00147] Suitable promoters for S. cerevisiae include those associated with the PGKI gene, GAL1 or GALIO genes, CYCI, PH05, TRP1, ADH1, ADH2, the genes for glyceraldehyde-3 -phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, triose phosphate isomerase, phosphoglucose isomerase, glucokinase, alpha-mating factor pheromone, [a mating factor pheromone], the PRBI promoter, the GUT2 promoter, the GPDI promoter, and hybrid promoters involving hybrids of parts of 5' regulatory regions with parts of 5' regulatory regions of other promoters or with upstream activation sites (e.g. the promoter of EP-A-258 067).
[00148] Convenient regulatable promoters for use in Schizosaccharomyces pombe are the thiamine-repressible promoter from the nmt gene as described by Maundrell (1990) J. Biol. Chem. 265, 10857-10864 and the glucose repressible jbpl gene promoter as described by Hoffman & Winston (1990) Genetics 124, 807-816. [00149] Methods of transforming Pichia for expression of foreign genes are taught in, for example, Cregg et al. (1993), and various Phillips patents (e.g. U.S. Pat. No. 4,857,467, incorporated herein by reference), and Pichia expression kits are commercially available from Invitrogen BV, Leek, Netherlands, and Invitrogen Corp., San Diego, Calif. Suitable promoters include AOX1 and AOX2. Gleeson et al. (1986) J. Gen. Microbiol. 132, 3459-3465 include information on Hansenula vectors and transformation, suitable promoters being MOX1 and FMD1; whilst EP 361 991, Fleer et al. (1991) and other publications from Rhone-Poulenc Rorer teach how to express foreign proteins in Kluyveromyces spp., a suitable promoter being PGKI.
[00150] The transcription termination signal is preferably the 3' flanking sequence of a eukaryotic gene which contains proper signals for transcription termination and polyadenylation. Suitable 3' flanking sequences may, for example, be those of the gene naturally linked to the expression control sequence used, i.e. may correspond to the promoter. Alternatively, they may be different in which case the termination signal of the S. cerevisiae ADHI gene is preferred.
[00151] In certain embodiments, the desired antigen-binding construct protein is initially expressed with a secretion leader sequence, which may be any leader effective in the yeast chosen. Leaders useful in S. cerevisiae include that from the mating factor alpha polypeptide (MFoc-1) and the hybrid leaders of EP-A-387 319. Such leaders (or signals) are cleaved by the yeast before the mature protein is released into the surrounding medium. Further such leaders include those of S. cerevisiae invertase (SUC2) disclosed in JP 62- 096086 (granted as 911036516), acid phosphatase (PH05), the pre-sequence of MFoc-1, 0 glucanase (BGL2) and killer toxin; S. diastaticus glucoarnylase II; S. carlsbergensis oc- galactosidase (MEL1); K. lactis killer toxin; and Candida glucoarnylase.
Post-translational modifications :
[00152] In certain embodiments are antigen-binding constructs described herein, which are differentially modified during or after translation. In some embodiments, the modification is at least one of: glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage and linkage to an antibody molecule or antigen-binding construct or other cellular ligand. In some embodiments, the antigen-binding construct is chemically modified by known techniques, including but not limited, to specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBH4; acetylation, formylation, oxidation, reduction; and metabolic synthesis in the presence of tunicamycin.
[00153] Additional post-translational modifications of antigen-binding constructs described herein include, for example, N-linked or O-linked carbohydrate chains, processing of N-terminal or C-terminal ends), attachment of chemical moieties to the amino acid backbone, chemical modifications of N-linked or O-linked carbohydrate chains, and addition or deletion of an N-terminal methionine residue as a result of procaryotic host cell expression. The antigen-binding constructs described herein are modified with a detectable label, such as an enzymatic, fluorescent, isotopic or affinity label to allow for detection and isolation of the protein. In certain embodiments, examples of suitable enzyme labels include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin; and examples of suitable radioactive material include iodine, carbon, sulfur, tritium, indium, technetium, thallium, gallium, palladium, molybdenum, xenon, fluorine. [00154] In specific embodiments, antigen-binding constructs described herein are attached to macrocyclic chelators that associate with radiometal ions.
[00155] In some embodiments, the antigen-binding constructs described herein are modified by either natural processes, such as post-translational processing, or by chemical modification techniques which are well known in the art. In certain embodiments, the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. In certain embodiments, polypeptides from antigen-binding constructs described herein are branched, for example, as a result of ubiquitination, and in some embodiments are cyclic, with or without branching. Cyclic, branched, and branched cyclic polypeptides are a result from posttranslation natural processes or made by synthetic methods. Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. (See, for instance, PROTEINS-STRUCTURE AND MOLECULAR PROPERTIES, 2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York (1993); POST-TRANSLATIONAL COVALENT MODIFICATION OF PROTEINS, B. C. Johnson, Ed., Academic Press, New York, pgs. 1-12 (1983); Seifter et al., Meth. Enzymol. 182:626-646 (1990); Rattan et al., Ann. N.Y. Acad. Sci. 663 :48-62 (1992)). [00156] In certain embodiments, antigen-binding constructs described herein are attached to solid supports, which are particularly useful for immunoassays or purification of polypeptides that are bound by, that bind to, or associate with proteins as described herein. Such solid supports include, but are not limited to, glass, cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride or polypropylene. Use of the antigen-binding constructs in the treatment of neurodegenerative diseases
[00157] In certain embodiments, provided is a method of treating a disease or disorder characterized by TDP-43 proteinopathy comprising administering to a subject in which such treatment, prevention or amelioration is desired, an TDP-43 antigen-binding construct described herein, in an amount effective to treat, prevent or ameliorate the disease or disorder.
[00158] "Disorder" or "disease" refers to any condition that would benefit from treatment with an anti-TDP-43 antibody or method as described herein. This includes chronic and acute disorders or diseases including those pathological conditions which predispose the mammal to the disorder in question. In a preferred embodiment, the diseases being treated with the antigen-binding constructs described herein are associated with TDP proteinopathy. These include, without limitation, amyotophic lateral sclerosis (ALS), Parkinson's disease, frontotemporal lobar degeneration (FTLD) motor neuron disease, Alzheimer's disease, dementia with Lewy bodies, Huntington's disease, Lewy body disease, mild cognitive impairment (MCI), or TDP-43 abnormalities triggered by nerve injury, brain trauma, brain ischemia (stroke).
[00159] The term "subject" refers to an animal, in some embodiments a mammal, which is the object of treatment, observation or experiment. An animal may be a human, a non-human primate, a companion animal (e.g., dogs, cats, and the like), farm animal (e.g., cows, sheep, pigs, horses, and the like) or a laboratory animal (e.g., rats, mice, guinea pigs, and the like).
[00160] The term "mammal" as used herein includes but is not limited to humans, non-human primates, canines, felines, murines, bovines, equines, and porcines. In some embodiments, the subject being treated with the anti-TDP-43 antigen-binding constructs is a mouse or a human.
[00161] "Treatment" refers to clinical intervention in an attempt to alter the natural course of the individual or cell being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include preventing occurrence or recurrence of disease, alleviation of symptoms, diminishing of any direct or indirect pathological consequences of the disease, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. In some embodiments, antigen-binding constructs as described herein are used to delay development of a disease or disorder.
[00162] Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. In some embodiments, constructs described herein are used to delay development of a disease or to slow the progression of a disease.
[00163] The term "effective amount" as used herein refers to that amount of construct being administered, which will accomplish the goal of the recited method, e.g., relieve to some extent one or more of the symptoms of the disease, condition or disorder being treated. The amount of the composition described herein which will be effective in the treatment, inhibition and prevention of a disease or disorder associated with aberrant expression and/or activity of a therapeutic protein can be determined by standard clinical techniques. In addition, in vitro assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. Effective doses are extrapolated from dose-response curves derived from in vitro or animal model test systems.
[00164] The TDP-43 antigen-binding constructs described herein are administered to the subject. Various delivery systems are known and can be used to administer an antigen- binding construct formulation described herein, e.g., encapsulation in liposomes, microparticles, microcapsules, recombinant cells capable of expressing the compound, receptor-mediated endocytosis (see, e.g., Wu and Wu, J. Biol. Chem. 262:4429-4432 (1987)), construction of a nucleic acid as part of a retroviral or other vector, etc. Methods of introduction include but are not limited to intradermal, intramuscular, intraperitoneal, intrathecal, intravenous, subcutaneous, intranasal, epidural, and oral routes. The compounds or compositions may be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, etc.) and may be administered together with other biologically active agents. Administration can be systemic or local.
[00165] In addition, in certain embodiments, it is desirable to introduce the antigen- binding construct compositions described herein into the central nervous system by any suitable route, including intraventricular and intrathecal injection; intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir, such as an Ommaya reservoir. Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent.
[00166] In a specific embodiment, it is desirable to administer the antigen-binding constructs, or compositions described herein locally to the area in need of treatment; this may be achieved by, for example, and not by way of limitation, local infusion during surgery, topical application, e.g., in conjunction with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers. Preferably, when administering a protein, including an antigen-binding construct, as described herein, care must be taken to use materials to which the protein does not absorb.
[00167] In another embodiment, the antigen-binding constructs or composition can be delivered in a vesicle, in particular a liposome (see Langer, Science 249: 1527-1533 (1990); Treat et al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez- Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid).
[00168] In yet another embodiment, the antigen-binding constructs or composition can be delivered in a controlled release system. In one embodiment, a pump may be used (see Langer, supra; Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987); Buchwald et al., Surgery 88:507 (1980); Saudek et al., N. Engl. J. Med. 321 :574 (1989)). In another embodiment, polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Fla. (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, New York (1984); Ranger and Peppas, J., Macromol. Sci. Rev. Macromol. Chem. 23 :61 (1983); see also Levy et al., Science 228: 190 (1985); During et al., Ann. Neurol. 25:351 (1989); Howard et al., J. Neurosurg. 71 : 105 (1989)). In yet another embodiment, a controlled release system can be placed in proximity of the therapeutic target, e.g., the brain, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, in Medical Applications of Controlled Release, vol. 2, pp. 115-138 (1984)).
Gene Therapy
[00169] In some embodiments, nucleic acid encoding antigen-binding constructs described herein can be administered in vivo to promote expression of its encoded protein, by constructing it as part of an appropriate nucleic acid expression vector and administering it so that it becomes intracellular, e.g., by use of a retroviral vector (see U.S. Pat. No. 4,980,286), or by direct injection, or by use of microparticle bombardment (e.g., a gene gun; Biolistic, Dupont), or coating with lipids or cell-surface receptors or transfecting agents, or by administering it in linkage to a homeobox-like peptide which is known to enter the nucleus (see e.g., Joliot et al., Proc. Natl. Acad. Sci. USA 88: 1864-1868 (1991)), etc. Alternatively, a nucleic acid can be introduced intracellularly and incorporated within host cell DNA for expression, by homologous recombination. [00170] In a specific embodiment, the nucleic acid encoding the antigen-binding construct is inserted into an adeno-associated virus (AAV) vector (see Patel et al., Molecular Therapy 22 (3) 498-510 (2014) and Example 12 herein). The viral vector may be administered to the subject systemically or locally, for example by intrathecal injection.
[00171] In certain embodiments an antigen-binding construct described herein is administered as a combination with antigen-binding constructs with non-overlapping binding target epitopes on TDP-43.
[00172] The amount of the antigen-binding construct which will be effective in the treatment, inhibition and prevention of a disease or disorder can be determined by standard clinical techniques. In addition, in vitro assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. Effective doses are extrapolated from dose-response curves derived from in vitro or animal model test systems. [00173] Also included herein is a method of preventing or delaying the onset of at least one symptom of a TDP-43 proteinopathy in a subject in need thereof comprising administering a therapeutically effective amount of an TDP-43 antigen binding construct described herein. In one embodiment, the subject is an experimental organism, such as, but not limited to, a transgenic mouse. In one embodiment, the subject is a human.
[00174] The antigen-binding constructs described herein may be administered alone or in combination with other types of treatments used for neurodegenerative diseases, such as Rilutek®. Methods of characterizing antigen-binding constructs
[00175] TDP-43 antigen-binding constructs described herein can be characterized using any in vivo or in vitro models of TDP-43 proteinopathies. A person skilled in the art understands that an TDP-43 antigen-binding construct can be characterized in a mouse model for TDP-43 proteinopathies, for example, one of the animal models for TDP-43 proteinopathies described in Swamp et al. Brain 134: 2610-2626 (2011). Swarup et al. 2011 describes three transgenic mouse models for TDP proteinopathies: wild type, G348C and A315T. These transgenic mice exhibit motor and cognitive impairment (as measured by the Barnes maze test, the step through passive avoidance test and the accelerating rotarod test). Additionally, the mice exhibit cytoplasmic TDP-43 -positive ubiquitinated inclusions, intermediate filament abnormalities, axonopathy and neuroinflammation. Additional animal models are described in Wegorzewska et al, Proc. Natl. Acad. Sci. U.S.A. 106 (2009), 18809-14; Gurney et al, Science 264 (1994), 1 772-75; Shan et al, Neuropharmacol. Letters 458 (2009), 70-74; Wils et al, Proc. Natl. Acad. Sci. USA. 106 (2010), 3858-63; Duchen and Strich, J. Neurol. Neurosurg, Psychiatry 31 (1968), 535-42; Dennis and Citron, Neuroscience 185 (2009), 745-50; Swamp et al, Brain 134 (2011), 2610-2626; Sgaz et al, J Clin invest. 121(2):726-38 (2011); Caccamo et al. Am J Pathol. 180(l):293-302 (2012), Cannon et al, Acta Neuropathol. 123(6):807-23 (2012), Custer et al, Hum Moi Genet. 19(9): 1741-55 (2010): and Tatom et al, oL Ther. 17 (2009), 607-613. These animal models may be used to evaluate the TDP-43 antigen-binding constructs described herein.
[00176] An experimental model of TDP-43 proteinopathy can be used in a preventative setting or it can be used in a therapeutic setting. In a preventative setting, the dosing of animals starts prior to the onset of the TDP-43 proteinopaihy or symptoms thereof. An TDP-43 antigen-binding construct described herein may be evaluated for its ability to prevent, reduce or delay the onset of TDP- 43 proteinopaihy or symptoms thereof. In a therapeutic model, the dosing of animals starts after the onset of TDP-43 proteinopaihy or a symptom thereof. In a therapeutic setting, an TDP-43 antigen-binding constructs is evaluated for its ability to treat, reduce or alleviate the TDP-43 proteinopaihy or a symptom thereof. Symptoms of the TDP-43 proteinopathies include, but are not limited to, accumulation of pathological TDP-43 deposits, pathological TDP-43 distribution, phosphorylated TDP-43, or insoluble TDP-43 fractions in the neurons, brain, spinal cord, cerebrospinal fluid or serum of the experimental object. A positive preventative or therapeutic outcome in any animal model of TDP-43 proteinopathies indicates that the particular TDP-43 antigen-binding construct can be used for preventative or therapeutic purposes in a subject other than the experimental model organism, for example, it can be used to treat TDP-43 proteinopathies in a human subject in need thereof.
[00177] In one embodiment, an TDP-43 antigen-binding construct can be administered to a TDP-43 proteinopathy mouse model and corresponding control wild type mice. The antigen-binding construct administered can be a murine antibody, or a human- murine chimera. The TDP-43 antigen-binding constructs can be administered by any means known in the art, for example, by intraperitoneal, intracranial, intramuscular, intrathecal, intravenous, subcutaneous, oral, and aerosol administration. Experimental animals can be given one, two, three, four, five or more doses of the TDP-43 antigen-binding constructs or a control composition, such as PBS. In one embodiment, experimental animals will be administered one or two doses of an TDP-43 antigen-binding construct. In another embodiment, the animals are chronically dosed with the TDP-43 antigen-binding constructs over several weeks or months. A skilled, artisan can readily design a dosing regimen that fits the experimental purpose, for example, dosing regimen for acute studies, dosing regimen for chronic studies, dosing regimen for toxicity studies, dosing regimen for preventative or therapeutic studies. The presence of the TDP-43 antigen-binding constructs in a particular tissue compartment of the experimental animals, for example, but not limited to, serum, blood, cerebrospinal fluid, brain or spinal cord tissue, can be established using well know methods of the art. In one embodiment, a TDP-43 antigen-binding construct is capable of penetrating the blood brain barrier. In another embodiment, a TDP-43 antigen- binding constructs is capable of entering neurons. By adjusting the dose of the TDP-43 antigen-binding construct and the dosing frequency, a desired concentration can be maintained in the experimental animals. Any effect of a TDP-43 antigen-binding construct as described herein in the TDP-43 proteinopathy models can be assessed by comparing the level, biochemical characteristics or distribution of TDP-43 in the treated and control animals. In one embodiment, a TDP-43 antigen-binding construct is capable of reducing the level, amount or concentration of TDP-43 inclusions in the brain or spinal cord in an animal model. The construct can reduce the level, amount or concentration of TDP-43 inclusions by at least about 5%, 10%, 20%, 30%, 50%, 70%, 90% or more. In another embodiment, a TDP-43 antigen-binding construct is capable of reducing the number or frequency of TDP-43 inclusion-positive neurons in the brain or spinal cord in an animal model, for example, by at least about 5%, 10%, 20%, 30%, 50%o, 70%, 90% or more. The effect of a TDP-43 antigen-binding construct can also be assessed by examining the distribution and biochemical properties of TDP-43 following administration. In one embodiment, a TDP-43 antigen-binding construct is capable of reducing the amount or concentration of cytoplasmic or nuclear TDP-43 protein in the brain or spinal cord of an animal model, for example, by at least about 5%, 10%, 20%, 30%, 50%, 70%, 90% or more, in another embodiment, it is capable of reducing the amount or concentration of neuritic TDP-43 protein in the brain or spinal cord of an animal model, for example, by at least about 5%, 10%, 20%, 30%, 50%, 70%. 90% or more, in a further embodiment, it can reduce the amount or concentration of phosphorylated TDP-43 protein in the brain or spinal cord in an animal model, for example, by at least about 5%, 10%, 20%, 30%, 50%, 70%), 90% or more. Phosphorylated TDP-43 can be detected using antibodies specific for pathologically phosphorylated forms of TDP-43, such as p403/p404 and p409/p410. Hasegawa et al., Ann Neurol, 64: 60-70 (2008). A TDP-43 antigen-binding construct can also alter, for example, reduce or increase TDP-43 concentration in the blood, serum or cerebrospinal fluid of an animal model, for example, by at least about 5%, 10%, 20%, 30%, 50%), 70%), 90%) or more, in one embodiment, the % reduction or increase is relative compared to the level, number, frequency, amount or concentration that existed before treatment, or to the level, number, frequency, amount or concentration that, exist in an untreated/control treated subject.
[00178] In one embodiment, a TDP-43 antigen-binding construct can prevent or delay the onset of at least one symptom of a TDP-43 proteinopathy in a subject. In one embodiment, a TDP-43 antigen-binding construct can reduce or eliminate at least one symptom of a TDP-43 proteinopathy in a subject. The symptom can be the formation of pathological TDP-43 deposits, phosphorylated TDP-43 deposits, or insoluble TDP-43 deposits. The symptom can also be the presence, or elevated concentration or amount, of TDP-43 in the serum, blood, urine or cerebrospinal fluid, wherein elevated concentration amount is compared to a healthy subject. In one specific embodiment, the symptom is the presence of TDP-43 -associated NF-kB. The symptom can be a neurological symptom., for example, loss of motor function or cognitive impairment. In one embodiment, memory impairment is assessed using the Barnes maze test or the step through passive avoidance test. In one embodiment motor function impairment is assessed using the accelerating rotarod test. In one embodiment, at least one symptom is reduced by at least about 5%, 10%, 15%, 20%, 30%, 50%, 70%, or 90%. In another embodiment, the latency time on the rotarod aparatus is significantly higher in a treated subject than in a control subject. In a specific embodiment, the rotarod latency time is increased by at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%. Kits and articles of manufacture
[00179] Also described herein are kits comprising one or more anti-TDP-43 antigen binding constructs. Individual components of the kit would be packaged in separate containers and, associated with such containers, can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale. The kit may optionally contain instructions or directions outlining the method of use or administration regimen for the antigen binding construct.
[00180] When one or more components of the kit are provided as solutions, for example an aqueous solution, or a sterile aqueous solution, the container means may itself be an inhalant, syringe, pipette, eye dropper, or other such like apparatus, from which the solution may be administered to a subject or applied to and mixed with the other components of the kit. [00181] The components of the kit may also be provided in dried or lyophilized form and the kit can additionally contain a suitable solvent for reconstitution of the lyophilized components. Irrespective of the number or type of containers, the kits described herein also may comprise an instrument for assisting with the administration of the composition to a patient. Such an instrument may be an inhalant, nasal spray device, syringe, pipette, forceps, measured spoon, eye dropper or similar medically approved delivery vehicle.
[00182] In another aspect described herein, an article of manufacture containing materials useful for the treatment, prevention and/or diagnosis of the disorders described above is provided. The article of manufacture comprises a container and a label or package insert on or associated with the container. Suitable containers include, for example, bottles, vials, syringes, IV solution bags, etc. The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition which is by itself or combined with another composition effective for treating, preventing and/or diagnosing the condition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). At least one active agent in the composition is a T cell activating antigen binding construct described herein. The label or package insert indicates that the composition is used for treating the condition of choice. Moreover, the article of manufacture may comprise (a) a first container with a composition contained therein, wherein the composition comprises an antigen-binding construct described herein; and (b) a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent. The article of manufacture in this embodiment described herein may further comprise a package insert indicating that the compositions can be used to treat a particular condition. Alternatively, or additionally, the article of manufacture may further comprise a second (or third) container comprising a pharmaceutically-acceptable buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes. Use of theTDP-43-binding constructs in the diagnosis and monitoring of TDP-43 proteinopathies
[00183] TDP-43 antigen-binding constructs may be used in the diagnosis of TDP-43 proteinopathies, particularly amyotrophic lateral sclerosis and/or frontotemporal lobar degeneration. Provided herein is the use of the TDP-43 antigen-binding constructs in the diagnosis and/or monitoring of a subject predisposed or suspected of developing a neurodegenerative disease or suffering from a neurodegenerative disease. The TDP-43 antigen-binding constructs may also be used in monitoring the efficacy of a treatment administered to a subject suffering from a TDP proteinopathy. [00184] Assay methods are provided in co-owned patent application published as WO 2012/174666A1 (herein incorporated by reference) for determining the level of interaction between a TDP-43 polypeptide or fragment thereof and a NF-kB p65 polypeptide or fragment thereof in a biological sample of the subject. Such assay methods may employ a TDP-43 binding construct described herein. An elevated level of interaction between TDP- 43 polypeptide or fragment thereof and p65 polypeptide or fragment thereof in the biological sample relative to a reference level of interaction between TDP-43 polypeptide or fragment thereof and p65 polypeptide or fragment thereof indicates that the subject is predisposed or suspected of developing a neurodegenerative disease or is suffering from a neurodegenerative disease. Further methods of using the TDP-43 antigen-binding constructs described herein to detect the association of TDP-43 and NF-kB are provided in the Examples below.
[00185] In another embodiment the TDP-43 antigen-binding constructs or nucleic acids encoding them may be used in a diagnostic composition as reagents in immuno- or nucleic acid-based diagnostic methods. The TDP-43 antigen-binding constructs as described herein are, for example, suited for use in immunoassays in which they can be utilized in liquid phase or bound to a solid phase carrier. Examples of immunoassays which can utilize the TDP-43 antigen-binding constructs as described herein are competitive and noncompetitive immunoassays in either a direct or indirect format. Examples of such immunoassays are the radioimmunoassay ( IA), the sandwich (immunometric assay), flow cytometry and the Western blot assay.
[00186] The antigen-binding constructs as described herein may be labeled for use in an assay. There are many different labels and methods of labeling known to those of ordinary skill in the art. Examples of the types of labels which can be used inone embodimentinclude enzymes, radioisotopes, colloidal metals, fluorescent compounds, chemiluminescent compounds, and bioluminescent compounds.
[00187] In a further embodiment, the TDP-43 antigen-binding constructs as described herein can also be used in a method for the diagnosis of a disorder in an individual by obtaining a sample from the tested individual which can be a blood sample, a lymph sample, cerebrospinal fluid, or a neural tissue biopsy sample and contacting the sample with a TDP-43 antigen-binding constructs under conditions enabling the formation of antibody-antigen complexes. The level of such complexes is then determined by methods known in the art. A level significantly higher than that formed in a control sample indicating the disease in the tested individual. One embodiment, is a method of diagnosing a TDP-43 proteinopathy in a subject, the method comprising: (a) assessing the level of TDP-43 in a sample from the subject to be diagnosed with an TDP-43 antigen-binding construct, and (b) comparing the level of TDP-43 observed to a reference standard that indicates the level of the TDP-43 in one or more control subjects, wherein a difference or similarity between the level of the TDP-43 and the reference standard indicates that the subject suffers from a TDP-43 proteinopathy. The subject to be diagnosed can be asymptomatic or preclinical for the disease. In one embodiment, the control subject has a TDP-43 proteinopathy, for example ALS or FTLD, wherein a similarity between the level of TDP-43 and the reference standard indicates that the subject, to be diagnosed has a TDP-43 proteinopathy.
[00188] The level of TDP-43 can be assessed by any suitable method known in the art comprising, e.g., analyzing TDP-43 by one or more techniques chosen from Western blot, immunoprecipitation, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), fluorescent activated cell sorting (FACS), or gel electrophoresis.
[00189] EXAMPLES
[00190] Below are examples of specific embodiments for carrying out the present invention. The examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperatures, etc.), but some experimental error and deviation should, of course, be allowed for. The practice of the present invention will employ, unless otherwise indicated, conventional methods of protein chemistry, biochemistry, recombinant DNA techniques and pharmacology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., T.E. Creighton, Proteins: Structures and Molecular Properties (W.H. Freeman and Company, 1993); A.L. Lehninger, Biochemistry (Worth Publishers, Inc., current addition); Sambrook, et al., Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Methods In Enzymology (S. Colowick and N. Kaplan eds., Academic Press, Inc.); Remington's Pharmaceutical Sciences, 18th Edition (Easton, Pennsylvania: Mack Publishing Company, 1990); Carey and Sundberg Advanced Organic Chemistry 3rd Ed. (Plenum Press) Vols A and B(1992).
[00191] EXAMPLE 1 : Generation of exemplary monoclonal antibodies against the TDP-43 RRMl domain of TDP-43 [00192] A series of exemplary monoclonal antibodies against a recombinant protein encoding the RRMl domain of TDP-43 were generated. The TDP-43 fragment used as antigen was generated and purified as follows. The EcoRl-Notl 428 bp hTDP43 cDNA fragment encoding RRMl was PCR-amplified and cloned into the pGEX-6P-l vector (GE Healthcare). This recombinant plasmid was used to transform the E.Coli host BL21 for the expression of the 136 aa protein encoding all the RRMl domain of hTDP43. The 15.68 kDa recombinant protein was subsequently purified using the Glutathione S-transferase (GST) gene fusion system (GE Healthcare). [00193] C57B16 mice were immunized with this polypeptide fragment, comprising amino acids 40-176 of TDP-43 (see Table A for sequence). The exemplary anti-TDP-43 monoclonal antibodies that were obtained using standard hybridoma technology yielded an immunodetection signal for TDP-43 protein when tested by immunoblotting after SDS- PAGE of spinal cord extracts from non-transgenic mice, as well as from transgenic mice over-expressing human TDP-43 (data not shown). Antibodies from three hybridoma clones CIO, G8 and E6 also detected TDP-43 on immunoblots of nuclear extracts from mouse microglial BV-2 cells fractionated by SDS-PAGE (shown in Figure 1).
[00194] EXAMPLE 2: Human recombinant F-κΒ p65 interacts directly with human recombinant TDP-43
[00195] BSA 0.8 ug/ml or human recombinant TDP-43 in serial dilutions from 0.8 ug/ml to 0.0125 ug/ml were prepared in PBS, loaded on ELISA microplates (6 wells per conditions) and incubated overnight. Human recombinant p65-His-Tag (Enzo Life Sciences) was prepared at the concentration of 0.2 ug/ml, added to all wells and incubated 2h. After 2h incubation in Blocking Buffer, anti-His-Tag-HRP (1 : 10.000) (Abeam) was prepared in Diluent Solutions, loaded on the plate and incubated 2h. Substrate Solution was added and Absorbance read at 450 nm. The results are shown in Figure 2. Values are expressed as mean ± sem.
[00196] EXAMPLE 3 : Interaction between recombinant TDP-43 and F-κΒ p65 is inhibited by exemplary bivalent monoclonal anti-RRMl -TDP-43 antibodies CIO, G8 and E6
[00197] Human recombinant TDP-43 was prepared at the concentration of 0.2 ug/ml, loaded on ELISA microplates and incubated overnight. p65-His-Tag (0.4 ug/ml) was mixed 1 : 1 with PBS, BSA (0.4 ug/ml), anti-TDP-43 polyclonal antibodies (Proteintech) (0.4 ug/ml IgG) or anti-RRMl -TDP-43 monoclonal antibodies (CIO, G8 or E6 monoclonalshaving an Fab/Fab format with an Fc domain) (0.4 ug/ml IgG) to reach the final concentration of 0.2 ug/ml p65 and 0.2 ug/ml interfering antibody. Mixed solutions were loaded on the plate (8 wells per condition) and incubated 2h. After 2h incubation in Blocking Buffer, anti-His-Tag-HRP (1 : 10.000) is prepared in Diluent Solutions, loaded on the plate and incubated 2h. Substrate Solution is added and Absorbance read at 450 nm. The results are shown in Figure 3, and demonstrate that all 3 of the monoclonal antibodies CIO, G8 and E6 block the interaction between TDP-43 and NF-κΒ p65 to a much greater extent than the polyclonal anti-TDP antibody. Values are expressed as mean ± sem.
[00198] EXAMPLE 4: Derivation of single chain anti-TDP-43 antibodies
[00199] The mRNAs were isolated from the appropriate hybridoma cell lines from Example 1 to derive cDNAs encoding scFv antibodies under the control of a CMV promoter. The variable regions of heavy chain (VH) and light chain (Vk) were amplified separately from first-strand cDNA by using a mixture of PCR primers and were cloned into the pBZUT7 (as described in Patel et al. Mol Then, 22 (3), 498-510 2014) vector and sequenced. The VH and Vk domains were assembled and linked together to yield a full- length scFv gene. The scFv gene was constructed in a VH-linker-Vk format together with a standard flexible 20-amino acid linker (Gly4Ser)3 and it was then subcloned upstream of the Myc-tagged Pswl scFVDl .3 Tagl expression vector (Patel et al. op. cit.) to generate scFv-TDP-43. Exemplary clones were then sequenced. The scFv generated contained a murine immunoglobulin (Ig) κ-secretory signal for efficient secretion and a human c-myc epitope to facilitate detection. A schematic drawing of these constructs is shown in Figure 4. [00200] EXAMPLE 5: Anti-TDP-43 antibodies having an scFv format localize in the cytoplasm and nucleus of HEK 293 cells, and are secreted
[00201] Hek 293 cells were transiently transfected with pScFv9 expression plasmid containing IgK domain, Myc-tag and a combination of the two VH and VK obtained from the E6 clone, i.e. VHlVk9, VHlVkl l, VH7Vk9 and VH7Vkl l . A schematic representation of the constructs is shown in Figure 4A. Cells were transfected with 4 μg of plasmid for 48h and then collected. Cytoplasmic and nuclear fractions were obtained and loaded on a 12% gel. Rabbit polyclonal anti-myc antibody (Abeam) was used to detect the ScFv antibodies inside the cells. Media of transfected cells were collected, centrifuged at 5000 rpm for 15 min at 4°C to eliminate debris and precipitated over-night at -20°C. The pellet was resuspended in loading buffer and loaded on 12% gel. The scFv antibodies were detected by blotting the membrane with mouse monoclonal anti-myc antibody (Santa Cruz). The results show that E6_VH1VK9 and E6_VH7VK9 SCFV antibodies localized in both the cytoplasm and the nucleus of Hek 293 cells (Figure 5). The scFv antibodies were also secreted into the medium (Figure 5).
[00202] EXAMPLE 6: anti-TDP-43 antibodies having an scFv format detect TDP-43 RRMl domain
[00203] Different concentrations of TDP-43 1-206 amino acid fragment, containing the RRMl domain were loaded onto membranes by dot blot. Membranes were incubated overnight with media from Hek293 cells that had been transfected with pScFv9 expression plasmid containing the nucleic acids encoding E6_VHlVk9 and E6_VH7Vk9. The myc signal was detected using anti-myc iTRP antibody incubation. The results, shown in Figure 6, demonstrate that E6_VHlVk9 and E6_VH7Vk9 scFv antibodies are able to recognize specifically TDP-43.
[00204] EXAMPLE 7: E6 VHlVk9 and E6 VH7Vk9 exemplary antigen-binding constructs in an scFv format block the interaction of TDP-43 with F-κΒ p65
[00205] An ELISA assay was performed as described in EXAMPLE 2 using the conditioned medium from E6_VHlVk9- and E6_VH7Vk9-expressing cells as a source of the antibodies. Medium from FIEK293 cells that had been transfected with an empty pScFv9 cells, or an irrelevant insert (D1.3) were used as controls. The results show that both E6_VHlVk9 and E6_VH7Vk9 are capable of blocking the TDP-43 interaction with F-κΒ p65 (Figure 7). The bivalent Fab/Fab format antibody E6 at a concentration of 0.4 ug/ml inhibited the TDP-43 interaction with F-κΒ p65 to an even greater extent, and a TDP-43 polyclonal antibody inhibited, but to a lesser degree than the monoclonals.
[00206] EXAMPLE 8: Antibodies expressed in HEK293 cells interact with TDP-43 intracellularly [00207] Cell lysates were made from E6_VHlVk9- and E6_VH7Vk9-expressing HEK293 cells. The lysates were exposed to polyclonal anti-TDP 43 to immunoprecipate cellular TDP-43. Immunopreciptates were resolved using PAGE. The results are shown in Figure 8, demonstrating that the scFv antibodies E6_VHlVk9 and E6_VH7Vk9 (detected by a myc tag) were co-immunoprecipitated with TDP-43. This demonstrates that the antigen-binding constructs E6_VH1VK9 and E6_VH7VK9 bound to intracellular TDP-43.
[00208] EXAMPLE 9: VHlVk9 antibody blocks the interaction of TDP-43 with F-KB p65 in HEK293 cells
[00209] Cell lysates were made from E6_VHlVk9-expressing FIEK293 cells which have been treated with T Fa 4 hours. The lysates were exposed to polyclonal anti-TDP 43 antibody to immunoprecipate cellular TDP-43. Immunoprecipitates were resolved using PAGE. Figure 9 shows an immunoblot in which an antibody against p65 was used to detect immunoprecipitates. The results show that decreased levels of F-κΒ p65 were present when VHlVk9 was expressed in the FIEK293 cells. This indicates that VHlVk9 interfered with the binding of TPD-43 to F-κΒ p65 in the cell.
[00210] EXAMPLE 10: Inhibition of F-κΒ activation by scFv exemplary antibodies against TDP-43 in cultured cell systems
[00211] A cell line was previously generated by stable transfection of BV-2 microglial cells with stable insertion of a luciferase reporter 4kBwt luciferase plasmid and subsequent selection with hygomycin (Swamp, 2011 J. Exp. Med. op cit). Expression plasmid vectors encoding scFv anti-TDP-43 antibodies were transfected into these BV-2 cultured cells and transiently expressed for 48 hours. During the final 4 hours, cells were exposed to either PBS (control) or 500ng/ml LPS. Cells were lysed with Glo Buffer (Promega) and 50 μΐ of lysates were loaded in replicates on a 96 well plate. Luciferase substrate was added following the assay procedures (Bright-Glo Luciferase Assay, Promega). RLU (relative light units) of luminescence were determined using an automatic plate reader and normalized on total proteins (^g) present in the well, as determined by protein quantification (Biorad).
[00212] The results shown in Figure 10 demonstrate the activation of the F-KB reporter gene was reduced after treatment with LPS in BV2 cells expressing either scFv antibody VH1VK9 or E6_VH7VK9. There was no effect of the antibodies on viability of BV2 cells (data not shown). We note that the scFv VH7-Vk9 antibody was more effective in reducing F-κΒ activity of BV2 cells than the scFv VHlVk9 antibody. The scFv VH7- Vk9 attenuated F-κΒ activity by 32% whereas scFv VH1 Vk9 reduced NF-κΒ activity by 13%. This is intriguing because these two scFv antibodies differ by only one amino acid, a Q (glutamine) instead of E (glutamic acid) in the scFv VH7-Vk9. Somehow this minor sequence variation appears to enhance the propensity of scFv E6_VH7Vk9 to distribute in the nucleus (as shown in Figure 5), a factor that may explain a more efficient inhibition of TDP-43 interaction with F-κΒ p65 in the nucleus.
[00213] EXAMPLE 11 : Expression of scFv antibodies in Neuro2A cells caused reduction in levels of nuclear TDP-43
[00214] Neuro 2A cells were transiently trasfected with E6_VHlVk9, E6_Vh7Vk9 or an empty vector as in Example 5. After 48 hours, nuclear extracts were obtained from the cells and the amount of nuclear TDP-43 was quantified by ponceau staining. The results are shown in Figure 11. Both E6_VHlVk9, E6_Vh7Vk9 reduced the amount of nuclear TDP-43 significantly. In ALS, there is an upregulation of TDP-43 mRNA and protein levels (Swarup et al. J Exp med 2011). This result suggests that anti-TDP-43 scFv antibodies might confer protection by attenuating the upregulation of TDP-43 in ALS.
[00215] EXAMPLE 12: Production of adeno-associated viral AAV vectors containing scFv antibodies [00216] The following protocol was used to produce pscAAV vectors containing E6- derived single chain antibodies. First, to produce unsecreted single chain antibodies (-IgK), a 773 bp fragment was obtained from pScFv9_E6VHlVk9 and pScFv9_E6VHVk9 by PCR introducing Xbal restriction site before the VH sequence and NotI at the end of the myc sequence. Digestion of the scAAV-CMV-EGFP (described in McCarty et al. Gene Ther. 8: 1248-1254, 2001) with Xbal and NotI restriction enzymes allowed replacing the EGFP sequence with E6VHlVk9(-IgK) and E6VH7Vk9(-IgK). Subsequently, the IgK sequence was obtained by pscFv9 plasmid using Hindlll and Pstl restriction enzymes. A Xbal/Pstl fragment containing Hindlll restriction site was inserted into corresponding restriction sites of pscAAV_E6VHlVk9_NS and E6VH7Vk9_NS plasmids before the VH sequence. Finally, pscAAV plasmids were digested with Hindlll and Pstl and the IgK sequence was inserted to obtain pscAAV_E6VHlVk9 and E6VH7Vk9 with a secretion signal. The secreted single chain antibodies were obtained by a standard method (Rabinowitz et al. J Virol., 76: 791-801(2002)). Briefly, the fragment encompassing the ScFv expression cassette in pscFv9-E6VHl Vk9 and E6VH7Vk9 was excised using Hindlll and EcoRV and cloned into the plasmid Bluescript SK(-) (Stratagene, Canada). It was then recloned as a Sall/Notl fragment into the Xhol/Notl digested scAAV-CMV-EGFP plasmid (McCarty et al. Gene Ther., 2011) replacing the EGFP encoding sequence and creating the pscAAV_E6VHl Vk9 and pscAAV_E6VH7Vk9 plasmids to be used in production of AAV recombinant viruses. Sequencing confirmed the correct insertions inside the plasmids.
[00217] EXAMPLE 13 : E6 scFv antibodies reduce TDP-43 insolubility in ethacrynic acid-treated cells [00218] Hek293 cells were transfected 72h in Optimem with 2 μg DNA and 5 μΐ
Lipofectamine 2000 reagent (Invitrogen) with E6 VI and E6 V7 scFv antibodies, empty plasmid or anti D1.3 scFv antibody and treated overnight with 50 μΜ ethacrynic acid (EA) to induce TDP-43 aggregation, or treated overnight with same volume of DMSO diluent as a control. The RIP A (radio- immunoprecipitation assay buffer) insoluble fraction was obtained. A representative western blot is shown in Figure 12A and a representative dot blot analysis of TDP-43 is shown in Figure 12B. The results show that both the E6 VI and E6 V7 scFv antibodies reduced the amount of insoluble TDP-43 detected after EA treatment (n=3/conditions). *, p<0,05 versus Empty. [00219] Immunofluorescence staining of the Hek293 transfected cells was conducted to localize TDP-43 in the cells (data not shown). In untransfected cells, TDP-43 mis- localized in the cytoplasm after EA treatment. However, in transfected cells expressing E6 VI and E6 V7 TDP-43 remained in the nucleus after EA treatment, avoiding cytoplasmic localization and aggregation.
[00220] EXAMPLE 14: E6 ScFv antibodies protect TDP-43 from Lysine
Acetyl ati on
[00221] Hek293 cells were transfected 48h in Optimem with 2 μg DNA and 5 μΐ
Lipofectamine 2000 reagent (Invitrogen) with E6 scFv antibodies VI and V7, empty plasmid or anti D1.3 scFv antibody and treated for 4 hours with 50ng/ml TNF alpha. Lysine acetylated proteins were immunoprecipitated using anti-acetyl-lysine antibody (Millipore) overnight in 300 μg total proteins lysate and the presence of lysine-acetylated TDP-43 was detected by western blotting for TDP-43 (Figure. 13). This result shows that that the E6 scFv antibodies protected TDP-43 from lysine acetylation. An empty transfection vector (EMT) was not protective, nor was a transfected control antibody D1.3. Lysine acetylation has been proposed as a novel post-translational modification controlling TDP-43 function and aggregation, and there is evidence that TDP-43 acetylation impairs RNA-binding and promotes accumulation of insoluble, hyper-phosphorylated TDP-43 species that largely resemble pathological inclusions in ALS and FTLD-TDP (Cohen T.J., Hwang A.W., Restrepo C.R., et al. Nat Com 2014).
[00222] The various embodiments described above can be combined to provide further embodiments. All of the U.S. patents, U.S. patent application publications, U.S. patent application, foreign patents, foreign patent application and non-patent publications referred to in this specification and/or listed in the Application Data Sheetare incorporated herein by reference, in their entirety. Aspects of the embodiments can be modified, if necessary to employ concepts of the various patents, application and publications to provide yet further embodiments. In the case of inconsistencies, the present disclosure will prevail. [00223] These and other changes can be made to the embodiments in light of the above- detailed description. In general, in the following claims, the terms used should not be construed to limit the claims to the specific embodiments disclosed in the specification and the claims, but should be construed to include all possible embodiments along with the full scope of equivalents to which such claims are entitled. The scope of the claims should not be limited by the preferred embodiments set forth in the examples, but should be given the broadest interpretation consistent with the description as a whole.

Claims

WE CLAIM
1. An antigen-binding construct that specifically binds a TAR-DNA binding protein 43kDa (TDP-43) comprising at least one heavy chain variable region VH comprising three VH complementarity determining regions (CDRs), wherein the VH comprises one, two or three of:
(a) a CDR selected from E6 VH1 CDR1, E6 VH7 CDR1, C10 VH3 CDR1 or C10 VH4 CDR1;
(b) a CDR selected from E6 VH1 CDR2, E6 VH7 CDR2, C10 VH3 CDR2 or C10 VH4 CDR2; and/or
(c) a CDR selected from E6 VH1 CDR3, E6 VH7 CDR3, C10 VH3 CDR3 or C10 VH4 CDR3.
2. The antigen-binding construct of claim 1, comprising one, two or three VH CDRs that are at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to:
(a) a CDRH1 selected from E6 VH1 CDR1, E6 VH7 CDR1, C10 VH3 CDR1 and C10 VH4 CDR1;
(b) a CDR2H2 selected from E6 VH1 CDR2, E6 VH7 CDR2, C10 VH3 CDR2 and C10 VH4 CDR2; and/or
(c) a VH CDRH3 selected from E6 VH1 CDR3, E6 VH7 CDR3, C10 VH3 CDR3 and C10_VH4 CDR3.
3. The antigen-binding construct of claim 1 or 2, comprising the VH of E6 VH1, E6 VH7, C10 VH3 or C10_VH4.
4. The antigen-binding construct of claim 3, wherein the VH is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the VH of E6_VH1, E6_VH7, C10_VH3 or CIO VH4.
5. The antigen-binding construct of any one of claims 1-4, further comprising a variable light chain region VL, wherein the VL comprises three VL CDRs, and wherein the VL comprises one, two or three of:
(a) a CDR selected from E6_VK9 CDRl and C10_VK3 CDRl;
(b) a CDR selected from E6_VK9 CDR2 and C10_VK3 CDR2; and/or
(c) a CDR selected from E6_VK9 CDR3 or C 10_VK3 CDR3.
6. The antigen-binding construct of claim 5, wherein the VL comprises one, two or three VL CDRs that are at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to:
(a) a CDR selected from E6_VK9 CDRl and C10_VK3 CDRl;
(b) a CDR selected from E6_VK9 CDR2 and C10_VK3 CDR2; and/or
(c) a CDR selected from E6_VK9 CDR3 or C 10_VK3 CDR3.
7. The antigen-binding construct of any one of claims 1-6, comprising the 6 CDRs selected from:
(a) the CDRl (SEQ ID NO. 7), CDR2 (SEQ ID NO. 8) and CDR3 (SEQ ID NO. 9), of E6 VH1 and the CDRl (SEQ ID NO. 7), CDR2 (SEQ ID NO. 8) and CDR3 (SEQ ID NO. 9) of E_6VK9;
(b) the CDRl (SEQ ID NO. 10), CDR2 (SEQ ID NO. 11) and CDR3 (SEQ ID N012) of E6 VH7 and the CDRl (SEQ ID NO. 7), CDR2 (SEQ ID NO. 8) and CDR3 (SEQ ID NO. 9) of E_6VK9;
(c) the CDRl (SEQ ID NO 16), CDR2 (SEQ ID NO. 17) and CDR3 (SEQ ID NO. 18) of C10 VH3, and the CDRl (SEQ ID NO. 22), CDR2 (SEQ ID NO. 23 and CDR3 (SEQ ID NO. 24) of C10_VK3; or
(d) the CDRl (SEQ ID N019), CDR2 (SEQ ID NO. 20) and CDR3 (SEQ ID NO. 21) of C10 VH4 and the CDRl (SEQ ID NO. 22), CDR2 (SEQ ID NO. 23 and CDR3 (SEQ ID NO. 24) of C10_VK3.
8. The antigen-binding construct of any one of claims 5-7 wherein the antigen-binding polypeptide comprises the VL of E6_VK9 or C10_VK3.
9. The antigen-binding construct of claim 8 wherein the VL is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the VL of E6_VK9 or C10_VK3.
10. The antigen binding construct of any one of claims 5-9, comprising the VH region of E6 VH1 or E6 VH7 and the VL region of E6_ VK9.
11. The antigen binding construct of any one of claims 5-9, comprising the VH region of C10 VH3 or C10 VH4 and the VL region of C10_ VK3.
12. The antigen-binding construct of any one of claims 5-11, comprising:
i) the VH of E6 VH7 and the VL of E6_ VK9;
ii) the VH of E6 VH1 and the VL of E6_ VK9;
iii) the VH of C 10 VH3 and the VL of C 10_ VK3 ; or iv) the VH of C 10 VH4 and the VL of C 10_ VK3.
13. The antigen-binding construct of any one of claims 5-12, wherein the construct comprises a peptide linker between the VH and VL, optionally wherein the linker comprises the amino acid sequence S S GGGGS GGGGS GGGGS (SEQ ID NO:47).
14. The antigen-binding construct of any one of claims 5-13, wherein the construct comprises at least one of E6_V1I7VK9, E6_Vhl VK9, C10_ VH3VK3 and C10_ VH4VK3.
15. The antigen-binding construct of any one of claims 5-13, wherein the construct comprises E6_Vh7VK9, E6_Vhl VK9, C10_ VH3VK3 or C10_ VH4VK3.
16. The antigen-binding construct of any one of claims 1-15, wherein the construct comprises a secretory signal peptide.
17. The antigen-binding construct of claim 16, wherein the secretory signal peptide is M G D N D I H F A F L S T G V H S Q V Q (SEQ ID NO:48).
18. The antigen-binding construct of any one of claims 5-17, wherein the construct has an scFv format.
19. The antigen-binding construct of any one of claims 5-18 wherein the construct has an Fab format.
20. The antigen binding construct of any one of claims 1-4, wherein the construct has a single domain antibody format.
21. The antigen-binding construct of any one of claims 5-17, wherein the construct has an (Fab')2 format.
22. The antigen-binding construct of any one of claims 1 to 21, wherein the construct comprises an Fc domain.
23. The antigen-binding construct of any one of claims 1 to 22, wherein the construct is humanized.
24. An antigen-binding construct that specifically binds to an RRM-1 domain of TDP-43, comprising a VH and a VL, wherein the construct, when expressed in a cell,
i) reduces the interaction of an intracellular TDP-43 polypeptide with an intracellular F-κΒ p65 polypeptide in Hek293 cells by 10% or more; or ii) reduces the activation of F-κΒ in the BV-2 cells in response to LPS by 10% or more; or
iii) reduces the level of nuclear TDP-43 in Neuro2A cells; or iv) reduces the lysine acetylation of TDP-43 in Hek293 cells in response to TNF alpha by 10% or more; or v) reduces the insolubility of TDP -43 in Hek293 cells incubated with ethacrynic acid.
25. The antigen-binding construct of claim 24, wherein the construct is any one of claims 5- 23.
26. An antigen-binding construct that blocks by 50% or more the binding of any of E6_VHlVk9, E6_VH7Vk9, C10_VH3Vk3 or C10_VH4Vk3 to TDP-43 or to the RRM-1 domain of TDP-43.
27. A pharmaceutical composition comprising the antigen-binding construct of any one of claims 1 to 25 and a pharmaceutically acceptable excipient.
28. A method of treating or preventing a disease characterized by TDP-43 proteinopathy in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of the antigen-binding construct of any one of claims 1-26 or the pharmaceutical composition of claim 27.
29. A method of treating or preventing a disease characterized by TDP-43 proteinopathy in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an adeno-associated viral (AAV) vector comprising at least one nucleic acid sequence that encodes at least one antigen-binding construct of any one of claims 1-26.
30. Use of the antigen-binding constructs of any one of claims 1-26 for the manufacture of a medicament for the treatment or prevention of a disease or disorder characterized by TDP- proteinopathy.
31. Use of the antigen-binding constructs of any one of claims 1-26 for the treatment or prevention of a disease or disorder characterized by TDP -proteinopathy.
32. The method or use of any one of claims 28-3 1 wherein the disease or disorder is selected from amyotrophic lateral sclerosis (ALS), Alzheimer's disease, motor neuron disease, Parkinson's disease, frontotemperal lobar degeneration (FTLD), mild cognitive impairment (MCI), Lewy body disease, brain trauma or cerebral ischemia.
33. The method or use of any one of claims 28-32 wherein the antigen-binding construct is administered in a pharmaceutical formulation.
34. A method of producing the antigen-binding constructs of any one of claims 1-26 comprising culturing a host cell under conditions suitable for expressing the antigen-binding construct, wherein the host cell comprises a polynucleotide encoding the antigen binding construct of any one of claims 1-25, and purifying the construct.
35. An polynucleotide or set of isolated polynucleotides comprising at least one nucleic acid sequence that encodes at least one of the antigen-binding construct of any one of claims 1 -26.
36. The polynucleotide of claim 35 wherein the polynucleotide or set of isolated polynucleotides is cDNA.
37. The polynucleotide or set of isolated polynucleotides of claim 35 or 36, comprising at least one nucleic acid sequence that encodes:
i) the VH of E6 VH7 and/or the VL of E6_ VK9;
ii) the VH of VK9and/or the VL of E6_ VK9;
iii) the VH of C 10 VH3 and/or the VL of C 10_ VK3 ; or
iv) the VH of C 10 VH4 and/or the VL of C 10_ VK3.
38. A polynucleotide or set of polynucleotides comprising a nucleic acid sequence that encodes E6_VH7VK9, E6 VH1 VK9, C 10_ VH3 VK3 or C 10_ VH4VK3.
39. A vector or set of vectors comprising one or more of the polynucleotides or sets of polynucleotides of any one of claims 35-38.
40. A vector or set of vectors comprising one of more of the polynucleotides or sets of polynucleotides of any one of claims 35-38 which is selected from a plasmid, a viral vector, a non-episomal mammalian vector, an expression vector, and a recombinant expression vector.
41. The vector of claim 39 or 40 wherein the vector is an adeno-associated viral (AAV) vector.
42. An isolated cell comprising a polynucleotide or set of polynucleotides according to any one of claims 35-38, or a vector or set of vectors of any one of claims 39 to 41.
43. A kit comprising the antigen-binding construct of any one of claims 1-26 and instructions for use.
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