IP Library › Granted Patent US 11,214,613

Granted Patent B2

US 11,214,613 · App. 16/616,832 · Granted Jan 4, 2022

Epitopes in the RNA recognition motif 1 (RRM1) of TDP-43 and misfolding-selective antibodies thereto

Inventors: Steven S. Plotkin (Vancouver, CA); Neil R. Cashman (Vancouver, CA); Xubiao Peng (Beijing, CN)

Assignee: The University of British Columbia

C07K16/18 C07K5/12 C07K14/4703 G01N33/6872 C07K2317/24 C07K2317/34 C07K2317/565 C07K2317/622 C07K2317/92

View Patent ↗

Loading inventors, assignments & file history…

Monitor This Case

Get email alerts when status or documents change.

Order Certified Copies

Most orders are placed with the USPTO same day — all within 24 business hours.

Order via The Patent Place →

Pre-filled with this patent's details

Quick Facts

Patent No.: US 11,214,613
App. No.: 16/616,832
Granted: Jan 4, 2022
Kind: B2

External Links

USPTO Patent Center↗ Full Patent PDF↗

Abstract

The disclosure pertains to conformational epitopes in TDP-43, antibodies thereto and methods of making and using immunogens and antibodies specific thereto.

Claims (225)

1. An antibody that selectively binds TDP-43, wherein the antibody comprises a light chain variable region and a heavy chain variable region, the heavy chain variable region comprising complementarity determining regions CDR-H1, CDR-H2 and CDR-H3, the light chain variable region comprising complementarity determining regions CDR-L1, CDR-L2 and CDR-L3 and with the amino acid sequences of said CDRs comprising the sequences:

CDR-H1: GYTFTDYS;

SEQ ID NO: 67

CDR-H2: INTETGEP;

SEQ ID NO: 68

CDR-H3: ASRRWYPYYFDY;

SEQ ID NO: 69

CDR-L1: TGAVTTSNY;

SEQ ID NO: 70

CDR-L2: GPN; and

SEQ ID NO: 71

CDR-L3: ALWYSNHWV;

SEQ ID NO: 72

CDR-H1: GFTFSDYY;

SEQ ID NO: 73

CDR-H2: ISNGGGST;

SEQ ID NO: 74

CDR-H3: AREGGTAWFAY;

SEQ ID NO: 75

CDR-L1: QSIVHSNGNTY;

SEQ ID NO: 76

CDR-L2: KVS; and

SEQ ID NO: 77

CDR-L3: FQGSHVPYT;

SEQ ID NO: 78

CDR-H1: GFTFSDYY;

SEQ ID NO: 73

CDR-H2: ISDGGSYT;

SEQ ID NO: 79

CDR-H3: ARDYYGSSSYTSGFAY;

SEQ ID NO: 80

CDR-L1: QSIVHSNGNTY;

SEQ ID NO: 76

CDR-L2: KVS; and

SEQ ID NO: 77

CDR-L3: FQGSHVPGT

SEQ ID NO: 81

CDR-H1: GYTFTDYS;

SEQ ID NO: 67

CDR-H2: INTETGEP;

SEQ ID NO: 68

CDR-H3: ARGYGNWFAY;

SEQ ID NO: 82

CDR-L1: SSVSSSY;

SEQ ID NO: 83

CDR-L2: STS; and

SEQ ID NO: 84

CDR-L3: HQYHRSPLT;

SEQ ID NO: 85

CDR-H1: GFTFSDFY;

SEQ ID NO: 86

CDR-H2: SRSKAHDYTT; and

SEQ ID NO: 87

CDR-H3: ARDTWYGSWFAY;

SEQ ID NO: 88

CDR-L1: QSIVHSNGNTY;

SEQ ID NO: 76

CDR-L2: KVS; and

SEQ ID NO: 77

CDR-L3: FQGSHVPPT;

SEQ ID NO: 92

CDR-H1: GYAFTNYL;

SEQ ID NO: 89

CDR-H2: INPGSGGT; and

SEQ ID NO: 90

CDR-H3: ARWGGNYSGYAMDY;

SEQ ID NO: 91

CDR-L1: QSIVHSNGNTY;

SEQ ID NO: 76

CDR-L2: KVS; and

SEQ ID NO: 77

CDR-L3: FQGSHVPPT

SEQ ID NO: 92.

2. The antibody of claim 1 , wherein the antibody selectively binds misfolded TDP-43 polypeptide compared to native TDP-43 polypeptide.

3. The antibody of claim 2 , wherein the antibody is at least 2 fold, 3 fold, at least 5 fold, at least 10 fold or at least 20 fold more selective for misfolded TDP-43 polypeptide compared to native TDP-43 polypeptide.

4. The antibody of claim 1 , wherein the antibody comprises:

a) a heavy chain variable region comprising: i) the amino acid sequence as set forth in SEQ ID NO: 46; ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 46, wherein the CDR sequences are as set forth in SEQ ID NO: 67, 68 and 69, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 67, 68 and 69; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 48, ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 48, wherein the CDR sequences are as set forth in SEQ ID NO: 70, 71 and 72, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 70, 71 and 7;

b) a heavy chain variable region comprising: i) the amino acid sequence as set forth in SEQ ID NO: 50; ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 50, wherein the CDR sequences are as set forth in SEQ ID NO: 73, 74 and 75, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 73, 74 and 75; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 52, ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 52, wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 78, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 78;

c) a heavy chain variable region comprising: i) the amino acid sequence as set forth in SEQ ID NO: 54; ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 54, wherein the CDR sequences are as set forth in SEQ ID NO: 73, 79 and 80, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 73, 79 and 80; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 56, ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 56, wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 81, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 81;

d) a heavy chain variable region comprising: i) the amino acid sequence as set forth in SEQ ID NO: 58; ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 58, wherein the CDR sequences are as set forth in SEQ ID NO: 67, 68 and 82, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 67, 68 and 82; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 60, ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 60, wherein the CDR sequences are as set forth in SEQ ID NO: 83, 84 and 85, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 83, 84 and 85;

e) a heavy chain variable region comprising: i) the amino acid sequence as set forth in SEQ ID NO: 62; ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 62, wherein the CDR sequences are as set forth in SEQ ID NO: 86, 87 and 88, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 86, 87 and 88; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 64, ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 64, wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 92, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 92; or

f) a heavy chain variable region comprises: i) the amino acid sequence as set forth in SEQ ID NO: 66; ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 66, wherein the CDR sequences are as set forth in SEQ ID NO: 89, 90 and 91, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 89, 90 and 91; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 64, ii) an amino acid sequence with at least 80% sequence identity to SEQ ID NO: 64, wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 92, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 92.

5. The antibody of claim 4 , wherein

a) the heavy chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 46 and/or the light chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 48;

b) the heavy chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 50 and/or the light chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 52;

c) the heavy chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 54 and/or the light chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 56;

d) the heavy chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 58 and/or the light chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 60;

e) the heavy chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 62 and/or the light chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 64; or

f) the heavy chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 66 and/or the light chain variable region comprises the amino acid sequence as set forth in SEQ ID NO: 64.

6. The antibody of claim 1 , wherein the antibody is a monoclonal antibody, humanized antibody and/or single chain antibody.

7. The antibody of claim 1 , wherein the antibody is a binding fragment selected from Fab, Fab′, F(ab′)2, scFv, dsFv, ds-scFv, dimers, nanobodies, minibodies, diabodies, and multimers thereof.

8. An immunoconjugate comprising the antibody of claim 1 and a detectable label or a transport moiety that facilitates transport across the blood brain barrier and/or into a cell.

9. A nucleic acid encoding i) an antibody or ii) an immunoconjugate that is a polypeptide comprising said antibody, the antibody comprising a light chain variable region and a heavy chain variable region, the heavy chain variable region comprising complementarity determining regions CDR-H1, CDR-H2 and CDR-H3, the light chain variable region comprising complementarity determining regions CDR-L1, CDR-L2 and CDR-L3 and with the amino acid sequences of said CDRs comprising the sequences:

CDR-H1: GYTFTDYS;

SEQ ID NO: 67

CDR-H2: INTETGEP;

SEQ ID NO: 68

CDR-H3: ASRRWYPYYFDY;

SEQ ID NO: 69

CDR-L1: TGAVTTSNY;

SEQ ID NO: 70

CDR-L2: GPN; and

SEQ ID NO: 71

CDR-L3: ALWYSNHWV;

SEQ ID NO: 72

CDR-H1: GFTFSDYY;

SEQ ID NO: 73

CDR-H2: ISNGGGST;

SEQ ID NO: 74

CDR-H3: AREGGTAWFAY;

SEQ ID NO: 75

CDR-L1: QSIVHSNGNTY;

SEQ ID NO: 76

CDR-L2: KVS; and

SEQ ID NO: 77

CDR-L3: FQGSHVPYT;

SEQ ID NO: 78

CDR-H1: GFTFSDYY;

SEQ ID NO: 73

CDR-H2: ISDGGSYT;

SEQ ID NO: 79

CDR-H3: ARDYYGSSSYTSGFAY;

SEQ ID NO: 80

CDR-L1: QSIVHSNGNTY;

SEQ ID NO: 76

CDR-L2: KVS; and

SEQ ID NO: 77

CDR-L3: FQGSHVPGT

SEQ ID NO: 81

CDR-H1: GYTFTDYS;

SEQ ID NO: 67

CDR-H2: INTETGEP;

SEQ ID NO: 68

CDR-H3: ARGYGNWFAY;

SEQ ID NO: 82

CDR-L1: SSVSSSY;

SEQ ID NO: 83

CDR-L2: STS; and

SEQ ID NO: 84

CDR-L3: HQYHRSPLT;

SEQ ID NO: 85

CDR-H1: GFTFSDFY;

SEQ ID NO: 86

CDR-H2: SRSKAHDYTT; and

SEQ ID NO: 87

CDR-H3: ARDTWYGSWFAY;

SEQ ID NO: 88

CDR-L1: QSIVHSNGNTY;

SEQ ID NO: 76

CDR-L2: KVS; and

SEQ ID NO: 77

CDR-L3: FQGSHVPPT;

SEQ ID NO: 92

CDR-H1: GYAFTNYL;

SEQ ID NO: 89

CDR-H2: INPGSGGT; and

SEQ ID NO: 90

CDR-H3: ARWGGNYSGYAMDY;

SEQ ID NO: 91

CDR-L1: QSIVHSNGNTY;

SEQ ID NO: 76

CDR-L2: KVS; and

SEQ ID NO: 77

CDR-L3: FQGSHVPPT

SEQ ID NO: 92.

10. A cell expressing the antibody of claim 1 .

11. A composition comprising the antibody of claim 1 , an immunoconjugate comprising said antibody or a cell expressing said antibody.

12. A kit comprising the antibody of claim 1 , an immunoconjugate comprising said antibody or a cell expressing said antibody.

13. A method of making the antibody of claim 1 , comprising administering an immunogen comprising a cyclic compound comprising: a TDP-43 peptide comprising: 1) TTE, 2) TTEQ (SEQ ID NO:1) or 3) TEQ and up to 6 TDP-43 contiguous residues, and a linker, wherein the linker is covalently coupled to the TDP-43 peptide N-terminus residue and the peptide C-terminus residue, wherein at least one amino acid in the TDP-43 peptide is an alternate conformation than T, E, and/or Q in a corresponding linear and/or native TDP-43 or a composition comprising said immunogen to a subject and isolating antibody and/or cells expressing antibody selective for the TDP-43 peptide in the cyclic compound of the immunogen administered.

14. A method of determining if a sample suspected of comprising misfolded TDP-43 polypeptides contains misfolded TDP-43 polypeptide the method comprising:

a) contacting the sample with the antibody of claim 1 under conditions permissive for forming an antibody: misfolded TDP-43 polypeptide complex; and

b) detecting the presence of any complex;

wherein the presence of detectable complex is indicative that the sample may contain misfolded TDP-43 polypeptide.

15. The method of claim 14 , wherein the sample comprises brain tissue extract, spinal cord tissue or cerebrospinal fluid (CSF).

16. The antibody of claim 1 , wherein the antibody comprises:

a) a heavy chain variable region comprising: i) the amino acid sequence as set forth in SEQ ID NO: 46; ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 46, wherein the CDR sequences are as set forth in SEQ ID NO: 67, 68 and 69, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 67, 68 and 69; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 48, ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 48, wherein the CDR sequences are as set forth in SEQ ID NO: 70, 71 and 72, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 70, 71 and 72;

b) a heavy chain variable region comprising: i) the amino acid sequence as set forth in SEQ ID NO: 50; ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 50, wherein the CDR sequences are as set forth in SEQ ID NO: 73, 74 and 75, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 73, 74 and 75; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 52, ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 52, wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 78, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 78;

c) a heavy chain variable region comprising: i) the amino acid sequence as set forth in SEQ ID NO: 54; ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 54, wherein the CDR sequences are as set forth in SEQ ID NO: 73, 79 and 80, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 73, 79 and 80; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 56, ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 56, wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 81, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 81;

d) a heavy chain variable region comprising: i) the amino acid sequence as set forth in SEQ ID NO: 58; ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 58, wherein the CDR sequences are as set forth in SEQ ID NO: 67, 68 and 82, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 67, 68 and 82; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 60, ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 60, wherein the CDR sequences are as set forth in SEQ ID NO: 83, 84 and 85, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 83, 84 and 85;

e) a heavy chain variable region comprising: i) the amino acid sequence as set forth in SEQ ID NO: 62; ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 62, wherein the CDR sequences are as set forth in SEQ ID NO: 86, 87 and 88, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 86, 87 and 88; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 64, ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 64, wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 92, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 92; or

f) a heavy chain variable region comprises: i) the amino acid sequence as set forth in SEQ ID NO: 66; ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 66, wherein the CDR sequences are as set forth in SEQ ID NO: 89, 90 and 91, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 89, 90 and 91; and/or wherein the antibody comprises a light chain variable region comprising i) the amino acid sequence as set forth in SEQ ID NO: 64, ii) an amino acid sequence with at least 90% or at least 90% sequence identity to SEQ ID NO: 64, wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 92, or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 76, 77 and 92.

17. A composition comprising the nucleic acid of claim 9 .

18. A kit comprising the nucleic acid of claim 9 .

19. The antibody of claim 1 , wherein the light chain variable region and the heavy chain variable region are fused.

20. The antibody of claim 1 , wherein the light chain variable region is encoded by an expression vector and the heavy chain variable region is encoded by another expression vector.

21. The antibody of claim 1 , wherein:

a) the heavy chain variable region amino acid sequence is encoded by the nucleotide sequence as set out in SEQ ID NO: 45 or a codon degenerate or optimized version thereof and/or wherein the light chain variable region amino acid sequence is encoded by the nucleotide sequence as set out in SEQ ID NO: 47 or a codon degenerate or optimized version thereof;

b) the heavy chain variable region amino acid sequence is encoded by the nucleotide sequence as set out in SEQ ID NO: 49 or a codon degenerate or optimized version thereof and/or the light chain variable region amino acid sequence is encoded by the nucleotide sequence as set out in SEQ ID NO: 51 or a codon degenerate or optimized version thereof;

c) the heavy chain variable region amino acid sequence is encoded by the nucleotide sequence as set out in SEQ ID NO: 53 or a codon degenerate or optimized version thereof and/or the light chain variable region amino acid sequence is encoded by the nucleotide sequence as set out in SEQ ID NO: 55 or a codon degenerate or optimized version thereof;

d) the heavy chain variable region amino acid sequence is encoded by the nucleotide sequence as set out in SEQ ID NO: 57 or a codon degenerate or optimized version thereof and/or the light chain variable region amino acid sequence is encoded by the nucleotide sequence as set out in SEQ ID NO: 59 or a codon degenerate or optimized version thereof;

e) the heavy chain variable region amino acid sequence is encoded by the nucleotide sequence as set out in SEQ ID NO: 61 or a codon degenerate or optimized version thereof and/or the light chain variable region amino acid sequence is encoded by a nucleotide sequence as set out in SEQ ID NO: 63 or a codon degenerate or optimized version thereof; or

f) the heavy chain variable region amino acid sequence is encoded by the nucleotide sequence as set out in SEQ ID NO: 65 or a codon degenerate or optimized version thereof and/or the light chain variable region amino acid sequence is encoded by the nucleotide sequence as set out in SEQ ID NO: 63 or a codon degenerate or optimized version thereof.

22. The antibody of claim 16 , wherein:

23. The nucleic acid of claim 9 , wherein the light chain variable region and the heavy chain variable region are fused.

24. The cell of claim 10 , wherein the cell is a hybridoma.

25. The method of claim 15 , wherein the sample is from a subject with or suspected of having amyotrophic lateral sclerosis (ALS) or frontotemporal dementia (FTD).

26. The composition of claim 17 , wherein the light chain variable region is encoded by a vector and the heavy chain variable region is encoded by another vector.

Assignments (1)

ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 21, 2020

From: PLOTKIN, STEVEN S.; CASHMAN, NEIL R.; PENG, XUBIAO

To: THE UNIVERSITY OF BRITISH COLUMBIA

Reel/Frame 051890/0503 →

Continuity (4)

Provisional Application 62595866 · Dec 7, 2017

Provisional Application 62570582 · Oct 10, 2017

Provisional Application 62512647 · May 30, 2017

Related Publication 20200165327A1 · May 28, 2020