CN117279937A - EPCAM binding molecules and uses thereof - Google Patents

EPCAM binding molecules and uses thereof Download PDF

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CN117279937A
CN117279937A CN202180093995.9A CN202180093995A CN117279937A CN 117279937 A CN117279937 A CN 117279937A CN 202180093995 A CN202180093995 A CN 202180093995A CN 117279937 A CN117279937 A CN 117279937A
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sequence
cdr
seq
cancer
gly
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法扎德·海利扎德
马苏德·塔耶比
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Boaades Biotech
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Boaades Biotech
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Priority claimed from PCT/US2021/063847 external-priority patent/WO2022133110A1/en
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Abstract

Disclosed herein are epithelial cell adhesion molecule (EpCAM) specific binding polypeptides. These binding polypeptides may be incorporated into Chimeric Antigen Receptors (CARs). Also disclosed herein are methods of using these binding polypeptides and/or CARs to treat, for example, cancer.

Description

EPCAM binding molecules and uses thereof
Cross Reference to Related Applications
The present application claims the benefit of priority from U.S. provisional patent application Ser. No. 63/127885, filed on 12 months 18 in 2020, and U.S. provisional patent application Ser. No. 63/2623310, filed on 8 months 10 in 2021, each of which is expressly incorporated herein by reference in its entirety.
Reference to sequence Listing
The present application is filed with a sequence listing in electronic format. The sequence listing is provided as a file titled bwgb007_seqlisting.txt, which was created and finally modified at day 12, month 16 of 2021, of size 23,340 bytes. The information in the electronic sequence listing is incorporated herein by reference in its entirety.
FIELD
Aspects of the present disclosure generally relate to epithelial cell adhesion molecule (EpCAM) specific binding polypeptides. These binding polypeptides can be incorporated into Chimeric Antigen Receptor (CAR) constructs for expression in immune cells. These binding polypeptides and CARs are useful for treating cancer.
Background
Chimeric Antigen Receptor (CAR) T cells and other adoptive cell therapies have been shown to be effective in the treatment of cancer. A CAR consisting of an extracellular antigen binding domain, a transmembrane domain, and an intracellular signaling domain enables direct killing of cancer cells based on cell surface antigen expression with minimal impact on normal cells that do not express the target antigen. The extracellular antigen-binding domain typically consists of an antibody or binding fragment or derivative thereof, such as a single chain variable fragment (scFv) or a single domain antibody (sdAb). There is a current need for improved extracellular antigen binding domains for use in CARs for the treatment of various cancers or other diseases.
Summary of the disclosure
Disclosed herein are binding polypeptides capable of binding an epithelial cell adhesion molecule (EpCAM). These binding polypeptides may be incorporated into Chimeric Antigen Receptors (CARs) that may be expressed by cells. In some embodiments, the binding polypeptide is a single domain antibody (sdAb).
In some embodiments, disclosed herein are EpCAM binding polypeptides comprising an immunoglobulin heavy chain variable domain comprising CDR-H1, CDR-H2, and CDR-H3. In some embodiments, CDR-H1 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS: 1-13. In some embodiments, CDR-H2 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS 14-26. In some embodiments, CDR-H3 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS 27-39. In some embodiments, CDR-H1 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS: 1-13, CDR-H2 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS: 14-26, and CDR-H3 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS: 27-39. In some embodiments, the immunoglobulin heavy chain variable domain comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS.40-52.
Also disclosed herein are nucleic acids encoding any of the EpCAM binding polypeptides disclosed herein.
Also disclosed herein are methods of treating cancer in a subject in need thereof. In some embodiments, the method comprises administering to the subject chimeric antigen receptor cells. In some embodiments, the chimeric antigen receptor cell is any one of the chimeric antigen receptor cells disclosed herein. In some embodiments, the chimeric antigen receptor cell comprises any one or more EpCAM binding polypeptides disclosed herein.
Embodiments of the invention provided herein are described by the following numbered alternatives:
1. an epithelial cell adhesion molecule (EpCAM) binding polypeptide comprising an immunoglobulin heavy chain variable domain comprising a CDR-H1, a CDR-H2, and a CDR-H3, wherein:
CDR-H1 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS 1-13;
CDR-H2 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS 14-26; and is also provided with
CDR-H3 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS.27-39.
2. The EpCAM binding polypeptide of claim 1, wherein:
1) CDR-H1 comprises the sequence of SEQ ID NO. 1, CDR-H2 comprises the sequence of SEQ ID NO. 14, and CDR-H3 comprises the sequence of SEQ ID NO. 27;
2) CDR-H1 comprises the sequence of SEQ ID NO. 2, CDR-H2 comprises the sequence of SEQ ID NO. 15, and CDR-H3 comprises the sequence of SEQ ID NO. 28;
3) CDR-H1 comprises the sequence of SEQ ID NO. 3, CDR-H2 comprises the sequence of SEQ ID NO. 16, and CDR-H3 comprises the sequence of SEQ ID NO. 29;
4) CDR-H1 comprises the sequence of SEQ ID NO. 4, CDR-H2 comprises the sequence of SEQ ID NO. 17, and CDR-H3 comprises the sequence of SEQ ID NO. 30;
5) CDR-H1 comprises the sequence of SEQ ID NO. 5, CDR-H2 comprises the sequence of SEQ ID NO. 18, and CDR-H3 comprises the sequence of SEQ ID NO. 31;
6) CDR-H1 comprises the sequence of SEQ ID NO. 6, CDR-H2 comprises the sequence of SEQ ID NO. 19, and CDR-H3 comprises the sequence of SEQ ID NO. 32;
7) CDR-H1 comprises the sequence of SEQ ID NO. 7, CDR-H2 comprises the sequence of SEQ ID NO. 20, and CDR-H3 comprises the sequence of SEQ ID NO. 33;
8) CDR-H1 comprises the sequence of SEQ ID NO. 8, CDR-H2 comprises the sequence of SEQ ID NO. 21, and CDR-H3 comprises the sequence of SEQ ID NO. 34;
9) CDR-H1 comprises the sequence of SEQ ID NO. 9, CDR-H2 comprises the sequence of SEQ ID NO. 22, and CDR-H3 comprises the sequence of SEQ ID NO. 35;
10 CDR-H1 comprising the sequence of SEQ ID NO. 10, CDR-H2 comprising the sequence of SEQ ID NO. 23, and CDR-H3 comprising the sequence of SEQ ID NO. 36;
11 CDR-H1 comprising the sequence of SEQ ID NO. 11, CDR-H2 comprising the sequence of SEQ ID NO. 24, and CDR-H3 comprising the sequence of SEQ ID NO. 37;
12 CDR-H1 comprising the sequence of SEQ ID NO. 12, CDR-H2 comprising the sequence of SEQ ID NO. 25, and CDR-H3 comprising the sequence of SEQ ID NO. 38; or alternatively
13 CDR-H1 comprising the sequence of SEQ ID NO:13, CDR-H2 comprising the sequence of SEQ ID NO:26, and CDR-H3 comprising the sequence of SEQ ID NO: 39.
3. The EpCAM binding polypeptide of alternatives 1 or 2 wherein the heavy chain variable domain comprises an amino acid sequence having at least 90%, 95%, 99% or 100% sequence identity to any sequence selected from SEQ ID NOs 40 to 52.
An epcam binding polypeptide comprising an immunoglobulin heavy chain variable domain comprising a CDR-H2, wherein CDR-H2 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOs 14-26.
5. The EpCAM binding polypeptide of claim 4 wherein the immunoglobulin heavy chain variable domain further comprises a CDR-H1, wherein CDR-H1 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOs 1-13.
6. The EpCAM binding polypeptide of claim 4 or 5 wherein the immunoglobulin heavy chain variable domain further comprises a CDR-H3, wherein CDR-H3 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOs 27-39.
7. The EpCAM binding polypeptide of any one of alternatives 1 to 6 wherein the EpCAM binding polypeptide is humanized.
8. The EpCAM binding polypeptide of any one of alternatives 1 to 7, wherein EpCAM binding polypeptide is a single domain antibody (sdAb).
9. A Chimeric Antigen Receptor (CAR) comprising the EpCAM binding polypeptide of any one of alternatives 1 to 8.
10. A Chimeric Antigen Receptor (CAR) cell comprising a CAR of alternative 9.
11. The CAR cell of alternative 10, wherein the CAR cell is a CAR T cell.
12. The CAR cell of claim 10 or 11, wherein the CAR cell comprises at least two binding polypeptides and the CAR cell is a multivalent CAR cell.
13. The CAR cell of any one of claims 10-12, wherein the CAR cell is derived from a subject or cell line.
14. The CAR cell of claim 13, wherein the subject has cancer.
15. The CAR cell of claim 14, wherein the cancer is breast cancer, colorectal cancer, kidney cancer, liver cancer, lung cancer, brain cancer, pancreatic cancer, bladder cancer, testicular cancer, prostate cancer, gastric cancer, ovarian cancer, head and neck cancer, gall bladder cancer, hematological malignancy, or any combination thereof.
16. A nucleic acid encoding a polypeptide comprising a sequence having at least 90%, 95%, 99% or 100% sequence identity to the EpCAM binding polypeptide of any one of alternatives 1 to 8 or the CAR of alternative 9.
17. A method of treating cancer in a subject in need thereof, comprising administering the CAR cell of any one of alternatives 10-15.
18. The method of claim 17, wherein the chimeric antigen receptor cells are autologous or allogeneic to the subject.
19. The method of claim 17 or 18, wherein the subject is a mammal.
20. The method of any one of claims 17-19, wherein the subject is a human.
21. The method of any one of claims 17-20, wherein the cancer is breast cancer, colorectal cancer, renal cancer, liver cancer, lung cancer, brain cancer, pancreatic cancer, bladder cancer, testicular cancer, prostate cancer, gastric cancer, ovarian cancer, head and neck cancer, gall bladder cancer, hematological malignancy, or any combination thereof.
22. The method of any one of claims 17-21, wherein the chimeric antigen receptor cells are administered parenterally.
Brief description of the drawings
In addition to the features described above, additional features and variations will be readily apparent from the following description of the drawings and exemplary embodiments. It should be understood that the drawings depict typical embodiments and are not intended to limit the scope.
FIG. 1 depicts an exemplary alignment of heavy chain variable domain CDRs disclosed herein.
Figure 2 depicts a bar graph showing the results of a cytotoxicity assay and an interferon gamma assay to show the in vitro efficacy of EpCAM CAR T cell candidates.
Fig. 3 depicts two line graphs showing the antitumor efficacy of an exemplary anti-EpCAM CAR T cell line B4T2-003 (' 003) against tumors in a cell line-derived xenograft (CDX) model of NCI-N87 (N87) gastric cancer and H2110 non-small cell lung cancer.
Fig. 4 depicts a line graph showing the results of a tumor re-challenge study showing the immunological memory of an exemplary anti-EpCAM CAR T cell line B4T 2-003.
Detailed description of the disclosure
Disclosed herein are binding polypeptides that are incorporated into chimeric antigen receptor cells. In some embodiments, the chimeric antigen receptor cell is a chimeric antigen receptor T cell (CAR-T cell). These CAR-ts can be constructed by methods conventionally known in the art. Binding polypeptides provide specificity for their respective tumor-associated antigens, enabling targeting of cancers expressing the tumor-associated antigens by CAR-T cells.
In some embodiments, the binding polypeptide is a single domain antibody (sdAb) disposed on the surface of a chimeric antigen receptor cell (e.g., CAR-T cell). The sdAb may be specific for a tumor-associated antigen or have binding affinity. In some embodiments, the tumor-associated antigen is an epithelial cell adhesion molecule (EpCAM).
Also disclosed herein are methods of treating cancer in a subject in need thereof by administering chimeric antigen receptor cells comprising one or more binding polypeptides disclosed herein. In some embodiments, the cancer may be breast cancer, colorectal cancer, renal cancer, liver cancer, lung cancer, brain cancer, pancreatic cancer, bladder cancer, testicular cancer, prostate cancer, gastric cancer, ovarian cancer, head and neck cancer, gall bladder cancer, hematological malignancy, or any combination thereof. In some embodiments, hematological malignancies may include leukemia, acute lymphoblastic leukemia, acute myelogenous leukemia, chronic lymphocytic leukemia, hairy cell leukemia, lymphoma, hodgkin's disease, non-hodgkin's lymphoma, or multiple myeloma. CAR-T cells may be derived from a subject for autologous therapy. Alternatively, the CAR-T cells may be derived from the same species as the subject for allogeneic therapy.
Definition of the definition
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which claimed subject matter belongs. It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of any subject matter claimed.
The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.
The articles "a" and "an" as used herein refer to one or more than one (e.g., to at least one) of the grammatical object of the article. By way of example, "an element" means one element or more than one element.
By "about" is meant an amount, level, value, number, frequency, percentage, dimension, size, quantity, weight, or length that varies by up to 30%, 25%, 20%, 15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% relative to a reference amount, level, value, number, frequency, percentage, dimension, size, quantity, weight, or length.
Throughout this specification, unless the context requires otherwise, the words "comprise", "comprises", "comprising" and "comprising" will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements. "consisting of …" is intended to include and be limited to anything following the phrase "consisting of …". Thus, the phrase "consisting of …" means that the listed elements are required or mandatory and that no other elements may be present. "consisting essentially of … (consisting essentially of)" is intended to include any element listed after the phrase and is limited to other elements that do not interfere with or contribute to the activity or action specified in the present disclosure for the listed elements. Thus, the phrase "consisting essentially of …" means that the listed elements are necessary or mandatory, but that other elements are optional and may or may not be present, depending on whether they substantially affect the activity or action of the listed elements.
As used herein, the terms "individual," "subject," and "patient" mean any mammal. In some embodiments, the mammal is a human. In some embodiments, the mammal is a non-human. None of these terms require or are limited to cases characterized by supervision (e.g., constant or intermittent) by a healthcare worker (e.g., doctor, registry nurse, nurse practitioner, physician's assistant, caregiver, or end-care worker).
The term "administering" includes enteral, oral, intranasal, parenteral, intravenous, intraperitoneal, intramuscular, intraarteriolar, intraventricular, intradermal, intralesional, intracranial, intrathecal or subcutaneous administration, or implantation of a sustained release device, such as a micro-osmotic pump, into a subject.
The term "nucleic acid" or "nucleic acid molecule" as used herein refers to polynucleotides, such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), oligonucleotides, fragments produced by the Polymerase Chain Reaction (PCR), and fragments produced by any of ligation, fragmentation, endonuclease action, and exonuclease action. The nucleic acid molecule may be composed of monomers that are naturally occurring nucleotides (e.g., DNA and RNA) or analogs of naturally occurring nucleotides (e.g., enantiomeric forms of naturally occurring nucleotides), or a combination of both. Nucleic acid monomers may be linked by phosphodiester linkages or analogs of such linkages. The one or more nucleic acids may be contained in a nucleic acid vector or nucleic acid construct (e.g., plasmid, virus, phage, cosmid, fosmid, phagemid, bacterial Artificial Chromosome (BAC), yeast Artificial Chromosome (YAC), or Human Artificial Chromosome (HAC)), which may be used for amplification and/or expression of the one or more nucleic acids in various biological systems. Typically, the vector or construct will also contain elements including, but not limited to, promoters, enhancers, terminators, inducers, ribosome binding sites, translation initiation sites, start codons, stop codons, polyadenylation signals, origins of replication, cloning sites, multiple cloning sites, restriction enzyme sites, epitopes, reporter genes, selectable markers, antibiotic selectable markers, targeting sequences, peptide purification tags, or accessory genes (accessorial genes), or any combination thereof.
The nucleic acid or nucleic acid molecule may comprise one or more sequences encoding different peptides, polypeptides or proteins. These one or more sequences may be linked adjacently in the same nucleic acid or nucleic acid molecule, or with additional nucleic acids therebetween, such as a linker, repeat or restriction enzyme site, or any other sequence of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200 or 300 bases in length, or any length within a range defined by any two of the foregoing lengths. The term "downstream" of a nucleic acid as used herein refers to a sequence following the 3' end of the preceding sequence, if the nucleic acid is double stranded, on the strand containing the coding sequence (sense strand). The term "upstream" of a nucleic acid as used herein refers to a sequence preceding the 5' end of the subsequent sequence, if the nucleic acid is double stranded, on the strand containing the coding sequence (sense strand). The term "grouped" on a nucleic acid as used herein refers to two or more sequences that occur directly or adjacent to additional nucleic acids therebetween, such as a linker, repeat, or restriction enzyme site, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, or 300 bases in length, or any other sequence of any length within a range defined by any two of the foregoing lengths, but generally not adjacent to the sequence encoding a functional or catalytic polypeptide, protein, or protein domain therebetween.
The term "codon-optimized" as used herein with respect to a nucleic acid refers to substitution of codons of the nucleic acid to enhance or maximize translation in a host of a particular species without altering the polypeptide sequence, based on species-specific codon usage bias and relative availability of each aminoacyl-tRNA in the target cell cytoplasm. Codon optimisation and techniques for performing such optimisation are known in the art. Those skilled in the art will appreciate that the level of gene expression depends on many factors, such as promoter sequences and regulatory elements. In this regard, many synthetic genes can be designed to increase their protein expression levels.
The terms "peptide", "polypeptide" and "protein" as used herein refer to macromolecules consisting of amino acids linked by peptide bonds. Various functions of peptides, polypeptides, and proteins are known in the art and include, but are not limited to, enzymes, structures, transport, defense, hormones, or signaling. Peptides, polypeptides and proteins are typically, but not always, biologically produced by using ribosomal complexes of nucleic acid templates, although chemical synthesis is also useful. By manipulating the nucleic acid templates, peptide, polypeptide, and protein mutations, such as substitutions, deletions, truncations, additions, replications, or fusions of more than one peptide, polypeptide, or protein, can be made. These fusions of more than one peptide, polypeptide or protein may be linked adjacently in the same molecule or with additional amino acids therebetween, such as linkers, repeats, epitopes or tags, or any other sequence of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200 or 300 bases in length, or any length within the range defined by any two of the foregoing lengths. The term "downstream" of a polypeptide as used herein refers to a sequence following the C-terminus of a previous sequence. The term "upstream" of a polypeptide as used herein refers to a sequence preceding the N-terminus of the subsequent sequence.
In some embodiments, the nucleic acid or peptide sequences presented herein and used in the examples are functional in a variety of biological systems including, but not limited to, human, mouse, rat, monkey, primate, cat, dog, rabbit, e.coli, yeast, and mammalian cells. In other embodiments, nucleic acid or peptide sequences sharing at least or less than 0%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identity, or any percentage within the range defined by any two of the foregoing identity percentages, with the nucleic acid or peptide sequences presented herein and used in the examples can also be used with little or no effect on the function of the sequences in the biological system. As used herein, the term "identity" refers to a nucleic acid or peptide sequence having the same overall sequence of nucleotides or amino acids as the template nucleic acid or peptide sequence, respectively, with specific changes within the sequence, such as substitutions, deletions, duplications or insertions. In some embodiments, two nucleic acid sequences sharing as little as 0%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity may encode the same polypeptide by comprising different codons encoding the same amino acid during translation.
As disclosed herein, sequences having% homology to any of the sequences disclosed herein are contemplated and may be used. The term "% homology" refers to the degree of conservation between two sequences when the three-dimensional structure of the two sequences is considered. For example, homology between two protein sequences may depend on structural motifs such as β -strands, α -helices and other folds, as well as their distribution throughout the sequence. Homology can be determined empirically or by structural measurement, in silico. In some embodiments, any sequence having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence homology to any sequence disclosed herein may be used. In some embodiments, any sequence having at least 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 substitutions, deletions, or additions relative to any of the sequences disclosed herein may be used, which may or may not affect the overall% homology.
As used herein, sequences having a certain% similarity to any of the sequences disclosed herein are contemplated and may be used. In some embodiments, these sequences may include peptide sequences, nucleic acid sequences, CDR sequences, variable region sequences, or heavy or light chain sequences. As understood in the art with respect to peptide sequences, "similarity" refers to a comparison of amino acids based on their properties, including, but not limited to, size, polarity, charge, pK, aromaticity, hydrogen bonding properties, or the presence of functional groups (e.g., hydroxyl, thiol, amine, carboxyl, etc.). The term "percent similarity" refers to the percentage of units (i.e., amino acids) that are identical between two or more sequences relative to the length of the sequences. When two or more sequences being compared are the same length,% similarity corresponds to that length. When two or more sequences being compared are of different lengths, deletions and/or insertions may be introduced to obtain an optimal alignment. The similarity of two amino acids may determine whether a substitution is conservative or non-conservative. Methods for determining conservation of amino acid substitutions are generally known in the art and may involve substitution matrices. Commonly used substitution matrices include BLOSUM45, BLOSUM62, BLOSUM80, PAM100, PAM120, PAM160, PAM200, PAM250, although other substitution matrices or methods may be used as deemed appropriate by those skilled in the art. When considering aspects of related sequences such as stringency, conservation, and/or differences (e.g., within the same species or more broadly), and sequence length in question, one substitution matrix may be preferred over other substitution matrices. As used herein, a peptide sequence having a certain% similarity to another sequence will have up to that% amino acids, which are identical or acceptable substitutions, as determined by the similarity assay method used. In some embodiments, sequences having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence similarity to any of the sequences disclosed herein may be used. In some embodiments, any sequence having at least 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 similar substitutions relative to any sequence disclosed herein may be used. As applicable to antibody sequences, these similar substitutions may be applicable to antigen binding regions (i.e., CDRs) or regions that do not bind antigen or are secondary only to antigen binding (i.e., framework regions).
The term "consensus sequence" as used herein with respect to sequences refers to a generic sequence that represents all the different permissible amino acid combinations at each position of a set of sequences. Consensus sequences may provide insight into conserved regions of related sequences, where units (e.g., amino acids or nucleotides) are identical in most or all sequences, as well as in regions that show differences between sequences. In the case of antibodies, the consensus sequence of the CDRs may indicate amino acids important or not necessary for antigen binding. It is envisioned that the consensus sequence may be prepared with any of the sequences provided herein, and that the resulting various sequences derived from the consensus sequence may be verified to have similar effects as the template sequence.
As used herein, the term "antibody" means a polypeptide chain-containing molecular structure that one of skill in the art imparts to it, and is further intended to include any polypeptide chain-containing molecular structure that has a specific shape that fits and recognizes an epitope, wherein one or more non-covalent binding interactions stabilize the complex between the molecular structure and the epitope.
The term "antibody library" refers to a collection of displayed antibodies and/or antibody fragments that are used to screen and/or combine into an intact antibody. Antibodies and/or antibody fragments may be displayed on ribosomes; displayed on phage; or displayed on the cell surface, in particular on the surface of yeast cells.
The term "competing" with respect to an antibody or binding polypeptide as used herein means that the first antibody or binding polypeptide, or antigen-binding portion thereof, binds to an epitope in a sufficiently similar manner to the binding of the second antibody or binding polypeptide, or antigen-binding portion thereof, such that the binding result of the first antibody or binding polypeptide to its cognate epitope is detectably reduced in the presence of the second antibody or binding polypeptide as compared to the binding of the first antibody or binding polypeptide in the absence of the second antibody or binding polypeptide. An alternative to the binding of the second antibody or binding polypeptide to its epitope also being detectably reduced in the presence of the first antibody or binding polypeptide, but this is not necessarily the case. Regardless of the mechanism by which such competition occurs (e.g., steric hindrance, conformational change, or binding to a consensus epitope or portion thereof), the skilled artisan will appreciate based on the teachings provided herein that such competing antibodies or binding polypeptides are encompassed and are useful in the methods disclosed herein.
Antibodies or binding polypeptides that "preferentially bind" or "specifically bind" (used interchangeably herein) to an epitope are terms well understood in the art, and methods for determining such specific or preferential binding are also well known in the art. A molecule is considered to exhibit "specific binding" or "preferential binding" if it reacts or associates with a particular cell or substance more frequently and/or more rapidly and/or for a longer duration and/or with a greater affinity than it reacts or associates with an alternative cell or substance. An antibody or binding polypeptide "specifically binds" or "preferentially binds" to a target if it binds to the target with greater affinity and/or avidity and/or more readily and/or for a longer duration than it binds to other substances.
The term "humanized" as applied to non-human (e.g., rodent or primate) antibodies is a hybrid immunoglobulin, immunoglobulin chain or fragment thereof that contains minimal sequence derived from a non-human immunoglobulin.
The term "single domain binding polypeptide" or "single domain antibody" (sdAb) as used herein refers to a polypeptide comprising an intact immunoglobulin domainOr other protein-folded single peptide chains that recognize the antigen (e.g., not bound to another peptide chain having disulfide bonds). The single domain binding polypeptide or sdAb may be derived from a typical heavy or light chain immunoglobulin chain, such as from a human, or from an alternative source, such as a dromedary (e.g., V H H) And cartilage fish (e.g. V NAR ). In some embodiments, the single domain binding polypeptide or sdAb comprises one, two, or three Complementarity Determining Regions (CDRs). In some embodiments, the single domain binding polypeptide or sdAb comprises one, two, or three of CDR1, CDR2, and CDR 3.
The term "single chain variable fragment" (scFv) as used herein is a fusion protein comprising the variable region of an immunoglobulin heavy chain (VH) and a light chain (VL), wherein VH and VL are covalently linked to form a VH: VL heterodimer. VH and VL are linked directly or through a peptide-encoding linker that links the N-terminus of VH to the C-terminus of VL, or links the C-terminus of VH to the N-terminus of VL. The linker is usually rich in glycine to obtain flexibility, and serine or threonine to obtain solubility. The scFv proteins retain the original immunoglobulin specificity despite removal of the constant region and introduction of the linker. Single chain Fv polypeptide antibodies may be expressed from nucleic acids comprising VH and VL coding sequences. In some embodiments, the VH and VL of the scFv each comprise one, two, or three CDRs. In some embodiments, the VH and VL of the scFv each comprise one, two, or three of CDR1, CDR2, and CDR 3.
In certain embodiments, the explicit delineation of CDRs and the identification of residues comprising the binding site of an antibody or binding polypeptide is accomplished by revealing the structure of the antibody or binding polypeptide and/or revealing the structure of an antibody-ligand complex. In certain embodiments, it may be achieved by any of a variety of techniques known to those skilled in the art, such as X-ray crystallography. In certain embodiments, various analytical methods may be employed to identify or mimic CDR regions. In certain embodiments, various analytical methods may be employed to identify or mimic CDR regions. Examples of such methods include, but are not limited to, the Kabat definition, the Chothia definition, the IMGT method (Lefranc et al, 2003) Dev Comp immunol. 27:55-77), computational programs such as Paratome (Kunik et al, 2012,Nucl Acids Res.W521-4), abM definition and conformational definition.
Kabat definition is a standard for numbering residues in antibodies and is commonly used to identify CDR regions. See, e.g., johnson & Wu,2000,Nucleic Acids Res, 28:214-8. The Chothia definition is similar to the Kabat definition, but the Chothia definition considers the location of certain structural loop regions. See, e.g., chothia et al, 1986, J.mol.biol.,196:901-17; chothia et al, 1989, nature,342:877-83.AbM defines an integrated suite of computer programs that use Oxford Molecular Group produced mimetic antibody structures. See, e.g., martin et al, 1989,Proc Natl Acad Sci (USA), 86:9268-9272; "AbM.TM., AComputer Program for Modeling Variable Regions of Antibodies," Oxford, UK; oxford Molecular, ltd. AbM defines the tertiary Structure of antibodies from primary sequences using a combination of knowledge databases and de novo computing (ab initio) methods, such as those described by Samuldrala et al, 1999, "Ab Initio Protein Structure Prediction Using a Combined Hierarchical Approach," PROTEINS, structure, function and Genetics suppl., 3:194-198. The contact definition is based on analysis of available complex crystal structures. See, e.g., macCallum et al, 1996, J.mol.biol.,5:732-45. In another approach, referred to herein as "conformational definition" of CDRs, the positions of the CDRs can be identified as residues that contribute enthalpy to antigen binding. See, e.g., makabe et al, 2008,Journal of Biological Chemistry,283:1156-1166. Still other CDR boundary definitions may not strictly follow one of the above methods, but still overlap with at least a portion of the Kabat CDRs, although they may be shortened or lengthened according to predictions or experimental findings that particular residues or groups of residues do not significantly affect antigen binding. As used herein, a CDR may refer to a CDR defined by any method known in the art, including combinations of methods. The methods used herein may utilize CDRs defined according to any of these methods. For any given embodiment containing more than one CDR, the CDR may be defined according to any one of Kabat, chothia, extended, IMGT, paratome, abM and/or conformational definitions or a combination of any of the foregoing.
The term "Chimeric Antigen Receptor (CAR)" as used herein refers to an engineered biological receptor that confers artificial specificity in immune cells against an antigen, such as a tumor-associated antigen. Exemplary immune cells in which the CAR may be used are T cells, but it is contemplated that the CAR may be engineered into any adaptable cytotoxic immune cell, including but not limited to T cells, natural Killer (NK) cells, natural Killer T (NKT) cells, dendritic cells, or macrophages. In this regard, any disclosure relating to CAR T cells may also be applicable to other immune cells comprising a CAR. At its core, the CAR comprises an extracellular antigen recognition domain (e.g., a tumor receptor ligand or antibody), a hinge, a transmembrane, and an intracellular signaling domain (an inner domain). Different combinations of these CAR components can result in different specificities and efficacy for certain cancer antigens.
As used herein, the term "treatment" or "treatment" (and as well understood in the art) means a method for obtaining a beneficial or desired result, including clinical results, of a subject condition. Beneficial or desired clinical results can include, but are not limited to, alleviation or amelioration of one or more symptoms or conditions, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, preventing spread or spread of disease, delaying or slowing of disease progression, amelioration or palliation of the disease state, diminishment of recurrence of the disease, and remission, whether partial or total, and whether detectable or undetectable. As used herein, "treatment" or "treatment" also includes prophylactic treatment. The method of treatment comprises administering to the subject a therapeutically effective amount of an active agent. The administering step may consist of a single administration or may comprise a series of administrations. The composition is administered to the subject in an amount and for a duration sufficient to treat the subject. The length of the treatment period depends on a variety of factors, such as the severity of the condition, the age and genetic characteristics of the subject, the concentration of the active agent, the activity of the composition used for treatment, or a combination thereof. It will also be appreciated that the effective dose of the agent for treatment or prevention may be increased or decreased during a particular treatment or prevention regimen. The variation in dosage may be caused by and become apparent from standard diagnostic assays known in the art. In some cases, long-term administration may be required.
The term "effective amount" or "effective dose" as used herein refers to the amount of the composition or compound that results in the specified effect that is observable. The actual dosage level of the active ingredient in the active compositions of the presently disclosed subject matter may be varied in order to administer an amount of the active composition or compound effective to achieve a specified response for a particular subject and/or application. The selected dosage level may vary based on a variety of factors including, but not limited to, the activity of the composition, the formulation, the route of administration, the combination with other drugs or treatments, the severity of the condition being treated, as well as the physical condition and prior medical history of the subject being treated. In some embodiments, a minimum dose is administered and the dose is increased to a minimally effective amount without dose limiting toxicity. Determination and adjustment of effective dosages, as well as an assessment of when and how such adjustments are made, are contemplated herein.
The term "administration" includes oral administration, topical contact, administration as a suppository, parenteral, intravenous, intraperitoneal, intramuscular, intralesional, intrathecal, intranasal, subcutaneous, or subcutaneous administration, or implantation of a sustained release device, such as a micro-osmotic pump, into a subject. Administration is by any route, including parenteral and transmucosal (e.g., buccal, sublingual, palate, gingival, nasal, vaginal, rectal, or transdermal). Parenteral administration includes, for example, intravenous, intramuscular, intraarteriolar, intradermal, subcutaneous, intraperitoneal, intraventricular and intracranial. Other modes of delivery include, but are not limited to, use of liposomal formulations, intravenous infusion, transdermal patches, and the like. By "co-administration" is meant that the first compound described herein is administered simultaneously with, immediately before, or shortly after the second compound described herein.
As used herein, the term "therapeutic target" refers to a gene or gene product that, upon modulation of its activity (e.g., by modulation of expression, biological activity, etc.), can provide a gene or gene product that modulates a disease phenotype. As used throughout, "modulation" is intended to mean an increase or decrease in the phenomenon shown (e.g., modulation of biological activity means an increase in biological activity or a decrease in biological activity).
As used herein, the terms "standard of care", "best practice" and "standard of care" refer to a treatment that is a suitable, appropriate, effective and/or widely used treatment for a certain disease that is accepted by a medical practitioner. The standard of care for a disease depends on many different factors including the biological effect of the treatment, the area or location in the body, the patient's state (e.g., age, weight, sex, genetic risk, other disabilities, secondary conditions), toxicity, metabolism, bioaccumulation, therapeutic index, dosage, and other factors known in the art. Determining the standard of care for a disease also depends on establishing safety and efficacy in clinical trials standardized by regulatory authorities such as the U.S. food and drug administration (US Food and Drug Administration), the international coordination center (International Council for Harmonisation), the canadian Health department (Health Canada), the european medicines administration (European Medicines Agency), the medical supplies administration (Therapeutics Goods Administration), the central medicines standards administration (Central Drugs Standard Control Organization), the national medicines administration (National Medical Products Administration), the medicines and medical instruments administration (Pharmaceuticals and Medical Devices Agency), the food and medicine safety department (Ministry of Food and Drug Safety) and the world Health organization (World Health Organization). The standard of care for the disease may include, but is not limited to, surgery, radiation, chemotherapy, targeted therapy, or immunotherapy.
The term "% w/w" or "% wt/wt" means the percentage expressed as the weight of the ingredient or agent compared to the total weight of the composition multiplied by 100.
Antigen binding polypeptides
Unless otherwise indicated, the Complementarity Determining Regions (CDRs) disclosed herein follow the IMGT definition. However, CDRs may also be interpreted alone or in the context of variable domains by Kabat, chothia or other definitions as understood by those skilled in the art.
Disclosed herein are epithelial cell adhesion molecule (EpCAM) binding polypeptides. In some embodiments, the EpCAM binding polypeptide comprises an immunoglobulin heavy chain variable domain comprising CDR-H1, CDR-H2, and CDR-H3. In some embodiments, CDR-H1 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS: 1-13. In some embodiments, CDR-H2 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS 14-26. In some embodiments, CDR-H3 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS 27-39. In some embodiments, CDR-H1 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS: 1-13; CDR-H2 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS 14-26; and CDR-H3 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS.27-39.
In some embodiments of the EpCAM binding polypeptide: 1) CDR-H1 comprises the sequence of SEQ ID NO. 1, CDR-H2 comprises the sequence of SEQ ID NO. 14, and CDR-H3 comprises the sequence of SEQ ID NO. 27; 2) CDR-H1 comprises the sequence of SEQ ID NO. 2, CDR-H2 comprises the sequence of SEQ ID NO. 15, and CDR-H3 comprises the sequence of SEQ ID NO. 28; 3) CDR-H1 comprises the sequence of SEQ ID NO. 3, CDR-H2 comprises the sequence of SEQ ID NO. 16, and CDR-H3 comprises the sequence of SEQ ID NO. 29; 4) CDR-H1 comprises the sequence of SEQ ID NO. 4, CDR-H2 comprises the sequence of SEQ ID NO. 17, and CDR-H3 comprises the sequence of SEQ ID NO. 30; 5) CDR-H1 comprises the sequence of SEQ ID NO. 5, CDR-H2 comprises the sequence of SEQ ID NO. 18, and CDR-H3 comprises the sequence of SEQ ID NO. 31; 6) CDR-H1 comprises the sequence of SEQ ID NO. 6, CDR-H2 comprises the sequence of SEQ ID NO. 19, and CDR-H3 comprises the sequence of SEQ ID NO. 32; 7) CDR-H1 comprises the sequence of SEQ ID NO. 7, CDR-H2 comprises the sequence of SEQ ID NO. 20, and CDR-H3 comprises the sequence of SEQ ID NO. 33; 8) CDR-H1 comprises the sequence of SEQ ID NO. 8, CDR-H2 comprises the sequence of SEQ ID NO. 21, and CDR-H3 comprises the sequence of SEQ ID NO. 34; 9) CDR-H1 comprises the sequence of SEQ ID NO. 9, CDR-H2 comprises the sequence of SEQ ID NO. 22, and CDR-H3 comprises the sequence of SEQ ID NO. 35; 10 CDR-H1 comprising the sequence of SEQ ID NO. 10, CDR-H2 comprising the sequence of SEQ ID NO. 23, and CDR-H3 comprising the sequence of SEQ ID NO. 36; 11 CDR-H1 comprising the sequence of SEQ ID NO. 11, CDR-H2 comprising the sequence of SEQ ID NO. 24, and CDR-H3 comprising the sequence of SEQ ID NO. 37; 12 CDR-H1 comprising the sequence of SEQ ID NO. 12, CDR-H2 comprising the sequence of SEQ ID NO. 25, and CDR-H3 comprising the sequence of SEQ ID NO. 38; or 13) CDR-H1 comprises the sequence of SEQ ID NO. 13, CDR-H2 comprises the sequence of SEQ ID NO. 26 and CDR-H3 comprises the sequence of SEQ ID NO. 39.
In some embodiments, the EpCAM binding polypeptide comprises an immunoglobulin heavy chain variable domain comprising CDR-H1, CDR-H2, and CDR-H3, wherein one or more of these CDRs are defined by a consensus sequence. The consensus sequences provided herein are derived from alignments of CDRs shown in fig. 1. However, it is contemplated that alternative alignments may be made (e.g., using global or local alignments, or using different algorithms, such as a hidden Markov model, a seed guide tree, a Needleman-Wunsch algorithm, or a Smith-Waterman algorithm, or other known methods), and thus alternative consensus sequences may be obtained (including those made with subsets of sequences provided herein).
In some embodiments, CDR-H1 is represented by formula X 1 X 2 X 3 X 4 X 5 X 6 X 7 X 8 Definition, wherein X 1 Is G; x is X 2 F, G, R, S or Y; x is X 3 Is I or T; x is X 4 F, S or Y; x is X 5 G, N, R or S; x is X 6 F, H, I, L, S, V or Y; x is X 7 D, N or Y; x is X 8 F, H, I, P, V or Y. In some embodiments, CDR-H1 comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identity to the consensus sequence. In some embodiments, CDR-H1 comprises a sequence with 0, 1, 2, 3, 4, 5, or 6 substitutions from the consensus sequence.
In some embodiments, CDR-H2 is represented by formula X 1 X 2 X 3 X 4 X 5 X 6 X 7 X 8 Definition, wherein X 1 Is I; x is X 2 S is; x is X 3 Is R; x is X 4 Is T; x is X 5 Is G; x is X 6 Is G; x is X 7 S is; x is X 8 Is T. In some embodiments, CDR-H2 comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identity to the consensus sequence. In some embodiments, CDR-H2 comprises a sequence with 0, 1, 2, 3, 4, 5, or 6 substitutions from the consensus sequence.
In some embodiments, CDR-H3 is represented by formula X 1 X 2 X 3 X 4 X 5 X 6 X 7 X 8 X 9 X 10 X 11 X 12 X 13 X 14 X 15 X 16 X 17 X 18 X 19 X 2 0 X 21 X 22 Definition, wherein X 1 Is amino acid-free or A; x is X 2 Is amino acid-free, A or V; x is X 3 Is amino acid-free, is G or R; x is X 4 Amino acid-free, A, D, G, H, L, Q or V; x is X 5 Amino acid-free, E, F, K, L, N, R or S; x is X 6 Amino acid-free, A, D, F, G, H, K, L, R or T; x is X 7 Amino acid-free, E, L, N, Q, R, S or T; x is X 8 Is amino acid-free, A, D, F, G, H, L, M, N, T, V or Y; x is X 9 A, D, G, N, P, Q, R, S or Y; x is X 10 A, H, I, L, N, P, R, T, V or W; x is X 11 Amino acid-free, M, Q, S or V; x is X 12 Amino acid-free, G, Q, R or V; x is X 13 Amino acid-free, A, G or T; x is X 14 Is amino acid-free, D, L, P or R; x is X 15 Amino acid-free, A, D, E, G, P or T; x is X 16 Amino acid-free, D, N, P, Q, S, T; x is X 17 Amino acid-free, A, E, G, I, L or N; x is X 18 Is amino acid-free, E, F, G, T, V or Y; x is X 19 A, D, G, I, P, Q, S, T or V; x is X 20 F, H, L or Y; x is X 21 Amino acid-free, D, G or S; x is X 22 Is amino acid-free or Y.
In some embodiments, CDR-H3 comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identity to the consensus sequence. In some embodiments, CDR-H3 comprises a sequence with 0, 1, 2, 3, 4, 5, or 6 substitutions from the consensus sequence.
Also disclosed herein are EpCAM binding polypeptides comprising an immunoglobulin heavy chain variable domain comprising a CDR-H2, wherein the CDR-H2 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOs 14-26. In some embodiments, the immunoglobulin heavy chain variable domain further comprises a CDR-H1, wherein the CDR-H1 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOS: 1-13. In some embodiments, the immunoglobulin heavy chain variable domain further comprises a CDR-H3, wherein the CDR-H3 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOS 27-39.
In some embodiments of the EpCAM binding polypeptide, the heavy chain variable domain comprises an amino acid sequence having at least 90%, 95%, 99% or 100% sequence identity to any sequence selected from SEQ ID NOs 40 to 52.
In some embodiments, the EpCAM binding polypeptide is humanized. In some embodiments, the EpCAM binding polypeptide is a single domain antibody (sdAb).
In some embodiments, the EpCAM binding polypeptide binds to EpCAM with a dissociation constant (KD) that is less than 1nM, 2nM, 5nM, 10nM, 15nM, 20nM, 30nM, 40nM, 50nM, 60nM, 70nM, 80nM, 90nM, 100nM, 200nM, 300nM, 400nM, 500nM, 600nM, 700nM, 800nM, 900nM, or 1000nM, or any KD within a range defined by any two of the foregoing KD.
Binding polypeptides disclosed herein may be obtained from a library of antibodies. In some embodiments, the antibody library is an immune antibody library, a natural antibody library, a synthetic antibody library, or a semisynthetic antibody library. In some embodiments, the antibody library comprises antibodies derived from humans or antibodies that are non-immunogenic in humans, or both. In some embodiments, the antibody library comprises humanized antibodies, e.g., from mice, rats, guinea pigs, rabbits Cats, dogs, cattle, horses, sheep, goats, horses, donkeys. In some embodiments, the antibody library comprises single domain antibodies (sdabs), nanobodies, V H H fragment, V NAR Fragments, single chain variable fragments (scFv), camelid antibodies, or cartilaginous fish antibodies, or any combination thereof. One exemplary library that may be used is a fully humanized, synthetic sdAb library, but any other antibody library that may be prepared or available may be used in the methods disclosed herein. In some embodiments, the antibody library comprises an sdAb. In some embodiments, the antibody library comprises at least 100, 500, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 20000, 30000, 40000, 50000, 60000, 70000, 80000, 90000, 100000, 500000, or 1000000 unique antibodies, or any number of antibodies within a range defined by any two of the foregoing numbers of antibodies.
The antibody library may be generated by calculation or using a machine learning process. Exemplary methods for computing antibody libraries include modifying one or more Complementarity Determining Regions (CDRs), such as CDR1, CDR2, or CDR3, or any combination thereof, into a universal V having synthetic diversity H And H frames. The diversity of CDRs is introduced by randomizing a library of sequences encoding antibodies with degenerate codons. For example, a library of NNK codons may be employed, wherein the NNK codons comprise N (25% mixture of A/T/C/G) and K (50% mixture of T/G). In some embodiments, the NNK codon library is constructed with all possible amino acids, or some amino acids (e.g., cysteines) and stop codon combinations are excluded. The NNK codon library can be substituted with other degenerate codon mixtures with minimal experimentation. In other embodiments, a library of antibodies can be generated using a trimeric codon mixture, which improves balanced representation of sense codons, while reducing the chance of stop codons, improving the efficiency of antibody generation and testing. In some embodiments, artificial intelligence based predictions can be used to randomize specific binding pockets of antibodies using available binding models or structural data.
In some embodiments, panning the antibody library comprises screening candidate binding polypeptides by phage display, yeast display, bacterial display, ribosome display, or mRNA display, or any combination thereof. In some embodiments, panning the antibody library comprises one or more rounds of selection, wherein the candidate binding polypeptide is selected for specificity for a cancer-associated antigen (e.g., epCAM) or a cell or tissue displaying a cancer-associated antigen. In some embodiments, the candidate binding polypeptides are selected under conditions including, but not limited to, tumor microenvironment-like conditions, immunosuppressive conditions, low or high pH, low or high oxygen concentration, low or high temperature, low or high viscosity, or any combination of the above, or the candidate binding polypeptides are selected for specificity for a modified or derivatized form of one or more cancer-associated antigens. In some embodiments, an immunosuppressive condition can include the presence of tumor-associated macrophages (TAMs), bone marrow-derived suppressor cells (MDSCs), tumor-associated neutrophils (TAN), cancer-associated fibroblasts (CAF), or other immunosuppressive cells, or the presence of adenosine, or both.
In some embodiments, the chimeric antigen receptor cells are from a cell line (e.g., jurkat). In some embodiments, the chimeric antigen receptor cells are derived from a subject. In some embodiments, the subject has cancer. In some embodiments, the subject has cancer, and the cancer expresses any one or more of the cancer-associated antigens disclosed herein (e.g., epCAM). In some embodiments, the cancer is breast cancer, colorectal cancer, renal cancer, liver cancer, lung cancer, brain cancer, pancreatic cancer, bladder cancer, testicular cancer, prostate cancer, gastric cancer, ovarian cancer, head and neck cancer, gall bladder cancer, hematological malignancy, or any combination thereof. In some embodiments, hematological malignancies may include leukemia, acute lymphoblastic leukemia, acute myelogenous leukemia, chronic lymphocytic leukemia, hairy cell leukemia, lymphoma, hodgkin's disease, non-hodgkin's lymphoma, or multiple myeloma. In some embodiments, the subject is a mammal, such as a human, cat, dog, mouse, rat, hamster, rodent, cow, pig, horse, goat, sheep, donkey, or monkey. In some embodiments, the subject is a human.
Chimeric Antigen Receptor (CAR) and cells
Also disclosed herein are Chimeric Antigen Receptors (CARs) comprising any one or more EpCAM binding polypeptides disclosed herein.
In some embodiments, the CAR comprises at least two binding polypeptides, and the CAR is a multivalent CAR. In some embodiments, the CAR comprises two binding polypeptides, and the CAR is a bivalent CAR. In some embodiments, the CAR comprises three binding polypeptides, and the CAR is a trivalent CAR.
In some embodiments, the CAR further comprises one or more signal peptides, linkers, hinges, transmembrane domains, costimulatory domains, signaling domains, cytoplasmic domains, functional signals, proliferative signals, anti-aging signals, anti-inhibitory receptors, tumor/cancer homing proteins, or regulatory molecules, or any combination thereof, of varying lengths and compositions. In some embodiments, the hinge comprises a CD3 ζ, CD4, CD8, or CD28 hinge, or a synthetic hinge of a calculated design having different lengths. In some embodiments, the transmembrane domain comprises a cd3ζ, CD4, CD8, or CD28 transmembrane domain, or a synthetic transmembrane domain of computational design. In some embodiments, the costimulatory domain comprises a CD8, CD28, ICOS, 4-1BB, OX40 (CD 134), CD27, CD40L, TLR, or other TNFR superfamily member or Ig superfamily member costimulatory domain, or other signaling via the cytoplasmic domain of IL-2Rβ, IL-15R- α, myD88, or CD40, or any other Toll-like receptor or IL-1 receptor signaling pathway member.
In some embodiments, the CARs disclosed herein are constructed by assembling a CAR expression construct from a mixture of nucleic acids encoding any one of the binding polypeptides disclosed herein and compatible nucleic acids encoding different CAR modules. In some embodiments, different combinations of CARs are generated for use in a CAR library for screening CAR efficacy (in vitro or in vivo). In some embodiments, the unique CAR is produced separately. In some embodiments, the CAR is specific for one target. In some embodiments, the CARs are specific for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 targets. In some embodiments, the CAR is bispecific or trispecific.
To construct any of the CARs disclosed herein, nucleic acids encoding binding polypeptides identified by panning an antibody library are assembled with other CAR modules into a CAR expression construct. In some embodiments, the CAR expression construct is assembled using a multi-fragment assembly reaction known in the art. One exemplary method of assembling a CAR expression construct involves using a type IIS restriction enzyme to generate a nucleic acid fragment having compatible protruding sequences and ligating the nucleic acid fragment with a ligase. When a type IIS restriction enzyme is cleaved outside its recognition site, multiple compatible nucleic acid fragments can be prepared simultaneously. In other embodiments, the CAR expression construct can be assembled by overlap extension PCR. It is contemplated that any other method of assembling a nucleic acid construct from more than one nucleic acid fragment may be employed. In some embodiments, the different CAR modules comprise a signal peptide, linker, hinge, transmembrane domain, costimulatory domain, activation domain, signaling domain, cytoplasmic domain, functional signal, proliferative signal, anti-aging signal, anti-inhibitor receptor, cancer homing protein, or regulatory molecule, or any combination thereof. Some exemplary hinges include a CD8 hinge, a CD28 hinge, an IgG1 hinge, or an IgG4 hinge. Some exemplary transmembrane domains include a cd3ζ transmembrane domain, a cd8α transmembrane domain, a CD4 transmembrane domain, a CD28 transmembrane domain, or an ICOS transmembrane domain. Some exemplary costimulatory domains include the CD8 costimulatory domain, the CD28 costimulatory domain, the 4-1BB costimulatory domain, the OX40 (CD 134) costimulatory domain, the ICOS costimulatory domain, the CD27 costimulatory domain, the CD40L costimulatory domain, the TLR costimulatory domain, the MYD88-CD40 costimulatory domain, or the KIR2DS2 costimulatory domain. In some embodiments, the different CAR modules are derived from CD8, CD28, 4-1BB, CD3 ζ, or any combination thereof. The CAR may also be modified with various additives including, but not limited to, cytokines, chemokines, cytokine receptors, chemokine receptors, antigen receptors or ligands, antibodies, or enzymes.
Also disclosed herein are Chimeric Antigen Receptor (CAR) cells comprising any of the CARs disclosed herein. In some embodiments, the CAR cell is a CAR-T cell. In some embodiments, the CAR cell is derived from a subject or cell line. In some embodiments, the subject has cancer. In some embodiments, the subject has cancer, and the cancer expresses any one or more of the cancer-associated antigens disclosed herein (e.g., epCAM). In some embodiments, the cancer is breast cancer, colorectal cancer, renal cancer, liver cancer, lung cancer, brain cancer, pancreatic cancer, bladder cancer, testicular cancer, prostate cancer, gastric cancer, ovarian cancer, head and neck cancer, gall bladder cancer, hematological malignancy, or any combination thereof. In some embodiments, hematological malignancies may include leukemia, acute lymphoblastic leukemia, acute myelogenous leukemia, chronic lymphocytic leukemia, hairy cell leukemia, lymphoma, hodgkin's disease, non-hodgkin's lymphoma, or multiple myeloma.
Nucleic acid
Also disclosed herein are nucleic acids encoding the polypeptides. In some embodiments, the polypeptide is a binding polypeptide. In some embodiments, the polypeptide is a single domain binding polypeptide. In some embodiments, the polypeptide is any one of the binding polypeptides disclosed herein. In some embodiments, the polypeptide comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to any one or more EpCAM binding polypeptides disclosed herein. In some embodiments, the polypeptide is any one of the CARs disclosed herein.
Any nucleic acid encoding a binding polypeptide may be prepared by recombinant DNA techniques, synthetic chemical techniques, or a combination thereof. For example, nucleic acid sequences encoding binding polypeptides may be cloned into expression vectors using standard molecular techniques known in the art. The sequences may be obtained from other vectors encoding the desired protein sequences, from PCR-generated fragments using the respective template nucleic acids, or by assembly of synthetic oligonucleotides encoding the desired sequences. In some embodiments, the expression vector can be a CAR expression vector, wherein it is provided to an immune cell to cause it to express the CAR. In some embodiments, the expression vector may be one suitable for large scale antibody or binding polypeptide production from which the peptide product may be isolated for further use.
Expression of the binding polypeptide or CAR can be confirmed by nucleic acid or protein assays known in the art. For example, the presence of transcribed mRNA that binds a polypeptide or CAR can be detected and/or quantified by conventional hybridization assays (e.g., northern blot analysis), amplification procedures (e.g., RT-PCR), SAGE (U.S. patent No. 5,695,937), and array-based techniques (see, e.g., U.S. patent nos. 5,405,783, 5,412,087, and 5,445,934), using probes complementary to any region of the polynucleotide encoding the binding polypeptide or CAR. Expression of the binding polypeptide or CAR can also be determined by detecting the expressed peptide. There are a variety of techniques available in the art for protein analysis. These include, but are not limited to, radioimmunoassays, ELISA (enzyme-linked immunosorbent assay), "sandwich" immunoassays, immunoradiometric assays, in situ immunoassays (using, for example, colloidal gold, enzyme or radioisotope labels), western blot analysis, immunoprecipitation assays, immunofluorescent assays, and SDS-PAGE.
Methods of use or treatment
Also disclosed herein are methods of treating cancer in a subject in need thereof. In some embodiments, the method comprises administering to the subject chimeric antigen receptor cells. In some embodiments, the method comprises administering any one of the chimeric antigen receptor cells disclosed herein. In some embodiments, the chimeric antigen receptor cells express and/or comprise any one or more EpCAM binding polypeptides disclosed herein. In some embodiments, the chimeric antigen receptor cell is a CAR-T cell. In some embodiments, the chimeric antigen receptor cells are derived from a subject and are autologous to the subject. In some embodiments, the chimeric antigen receptor cell is allogeneic to the subject. In some embodiments, the chimeric antigen receptor cells are from a cell line (e.g., jurkat). In some embodiments, the subject is a mammal, such as a human, cat, dog, mouse, rat, hamster, rodent, cow, pig, horse, goat, sheep, donkey, or monkey. In some embodiments, the subject is a human. In some embodiments, the subject has cancer, and the cancer expresses any one or more of the cancer-associated antigens disclosed herein (e.g., epCAM). In some embodiments, the cancer is breast cancer, colorectal cancer, renal cancer, liver cancer, lung cancer, brain cancer, pancreatic cancer, bladder cancer, testicular cancer, prostate cancer, gastric cancer, ovarian cancer, head and neck cancer, gall bladder cancer, hematological malignancy, or any combination thereof. In some embodiments, hematological malignancies may include leukemia, acute lymphoblastic leukemia, acute myelogenous leukemia, chronic lymphocytic leukemia, hairy cell leukemia, lymphoma, hodgkin's disease, non-hodgkin's lymphoma, or multiple myeloma. In some embodiments, the chimeric antigen receptor cells are administered parenterally.
In some embodiments, the chimeric antigen receptor cells are administered once daily, twice daily, three times daily, or more. In some embodiments, the chimeric antigen receptor cells are administered daily, every day, every other day, every fifth day, weekly, every other week, every second week, every third week, monthly, twice a month, three or more times a month. In some embodiments, the immune cells are administered for at least 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months, 18 months, 2 years, 3 years, or more.
In some embodiments, the amount of a given reagent corresponding to such an amount varies depending on factors such as: the particular compound, the severity of the disease, the characteristics of the subject or host in need of treatment (e.g., body weight), but still are routinely determined in a manner known in the art, including, for example, the particular agent being administered, the route of administration, and the subject or host being treated, depending on the particular circumstances surrounding the case. In some cases, the desired dose is conveniently presented as a single dose or as divided doses administered simultaneously (or over a short period of time) or at appropriate intervals, for example as two, three, four or more sub-doses per day.
The scope of administration is merely suggestive, as the number of variables for an individual treatment regimen is large and a substantial deviation from these recommended values is not uncommon. Such dosages vary depending on a number of variables, which are not limited to the activity of the compound used, the disease or condition to be treated, the mode of administration, the needs of the individual subject, the severity of the disease or condition to be treated, and the judgment of the practitioner.
In some embodiments, toxicity and therapeutic efficacy of such treatment regimens are determined by standard pharmaceutical procedures in cell cultures or experimental animals, including, but not limited to, determination of LD50 (the dose lethal to 50% of the population) and ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and is expressed as the ratio between LD50 and ED 50. Compounds exhibiting high therapeutic indices are preferred. Data obtained from cell culture assays and animal studies are used in formulating a range of dosage for use in humans. The dosage of such a compound is preferably within a circulating concentration range that includes the ED50 with minimal toxicity. The dosage will vary within this range depending upon the dosage form employed and the route of administration utilized.
Examples
Some aspects of the embodiments discussed above are disclosed in more detail in the following examples, which are not intended to limit the scope of the present disclosure in any way. Those skilled in the art will appreciate that many other embodiments are also within the scope of the invention, as described above and in the claims.
Example 1 method
Plasmid preparation and quality inspection (QC)
Maxi plasmid purification kit (Zymo, D4203) was used for CAR plasmid preparation. Plasmid concentration and quality were analyzed by Nanodrop (260/280 ratio and 260/230 ratio) and ToxinSensor Chromogenic LAL endotoxin assay (Genescript, L00350). The quality plasmid DNA will have an A260/A280 ratio of 1.8-2.0, an A260/A230 ratio of greater than 2.0 and an endotoxin of less than 0.1 EU/. Mu.g.
Plasmid assembly and QC
All CARs were synthesized by Genewiz. The synthetic single domain antibody gene encoding the antibody that binds EpCAM was cloned into the pLenti vector and the construct was confirmed using Sanger sequencing. The CAR construct contains a signal peptide (e.g., CD8 signal peptide), a hinge (e.g., CD8 alpha handle (walk)), a transmembrane domain (e.g., CD8 transmembrane domain or CD28 transmembrane domain), and a signaling domain (e.g., 4-1BB costimulatory domain or CD3 zeta signaling domain), and an anti-EpCAM sdAb.
To monitor CAR expression levels, the expression cassette of the CAR plasmid can also be engineered to express a fluorescent egfp+t2a self-cleaving peptide sequence. Alternatively, the truncated CD19 or truncated EGFR cassette can be used for monitoring by antibody detection. Human sequences (e.g., CD8, 4-1BB, CD3 ζ) are available on GenBank.
Virus production and titration
To generate lentiviruses with anti-EpCAM CAR constructs, human embryonic kidney 293T (HEK 293T) cells were co-transfected with a slenti transfer plasmid encoding the CAR transgene together with one or more necessary packaging plasmids (i.e., encoding Gag, pol, rev, VSVG and optionally Tat). Supernatants from HEK293T cultures were collected 48 or 72 hours post-transfection, centrifuged and filtered with a 0.45 μm filter.
Virus titration was performed in Jurkat cells transduced with a diluted lentiviral harvest. After 48 hours, transduced Jurkat cells were stained with biotinylated recombinant protein L and Phycoerythrin (PE) -conjugated streptavidin and anti-EpCAM CAR abundance was measured by flow cytometry.
T cell transduction and expansion
Human PBMCs were isolated from peripheral blood of healthy human donors by density gradient centrifugation with Lymphoprep reagent (StemCell Technologies). PBMC were used at 1X 10 6 Individual cells/mL were resuspended in X-VIVO 15 serum-free hematopoietic medium (Lonza, 04-418 QCN) with 10ng/mL IL-2 (Novoprotein, GMP-CD 66) and 10ng/mL IL-7 (Novoprotein, GMP-CD 47). PBMC were stimulated with 50ng/mL anti-CD 3 antibody (Novoprotein, GMP-A018) for 24 hours. Then, using a resist EpCAM CAR lentiviruses (MOI 1-10) transduced PBMC and amplified in appropriate flasks for 9-10 days in RPMI 1640 basal medium supplemented with 10% fetal bovine serum. T cells were allowed to stand at 37 ℃ for 24 hours prior to any assay. CAR surface levels, CD3 and CD4/CD8 ratios (using antibodies 317344, 301012 and 317412 from bioleged) were measured 12 or 14 days after initial stimulation of PBMCs with anti-CD 3 antibodies.
Cryopreservation and thawing of T cells
After 14 days of CAR-T expansion, anti-EpCAM CAR-T cells were centrifuged and the supernatant was discarded. Cell pellet at 5X 10 7 Viable cell density of individual cells/mL was resuspended in chilled cryoston CS10 (StemCell Technologies, 07930). An aliquot of the cell suspension was dispensed into a frozen vial. The frozen vials were cooled at a rate of 1 c/min. Frozen cells were transferred to liquid nitrogen.
For thawing, the cells were quickly thawed in a 37 ℃ water bath with gentle agitation. The thawed cells were transferred to a 50mL conical tube and washed by dropwise addition of 20mL fresh growth medium. Cells were centrifuged and at 1X 10 6 Cell density per mL was resuspended in X-VIVO 15 medium.
Cytotoxicity assays
Cytotoxicity against EpCAM CAR T cells was determined by a standard luciferase-based assay. Briefly, in X-VIVO 15 medium, 2X 10 with a total volume per well of 100. Mu.L was used 4 White wall 96-well plates of individual target cells, with the indicated effectors: target ratio, target cells expressing firefly luciferase were co-cultured with CAR-T cells in triplicate. Individual target cells as controls were seeded at the same cell density. After 48 hours of co-cultivation, 100. Mu.L of luciferase substrate (ONE-Glo, promega) was added directly to each well. The emitted light was detected with a light plate reader.
In a similar luciferase-based cytotoxicity assay, target cancer cells engineered to overexpress luciferase are prepared in cell culture medium (e.g., RPMI) and expressed at 5×10 4 From 5 to 10 6 Individual cells were seeded into 96-well plates at a volume of 100 μl/well and incubated for 24 hours at 37 ℃. Then, with different effectors: target (E: T) ratio (e.g., 5:1, 1:1, and 1:5), CAR T cells were seeded at 100 μl/well in the corresponding wells with CAR T cells. The co-cultures were then incubated at 37℃for 24 or 48 hours. Subsequently, cells were treated with a luciferase assay system (Promega, E1501) using a plate reader according to the manufacturer's instructions. Luminescence was read in endpoint mode for 10 seconds using a BioTek Synergy H4 hybridization microplate reader. Luciferase activity of digitonin-treated cells was used as maximum cell death, and untreated cells as spontaneous cell death, using the formula%specific lysis = 100%x [ (experimental luminescence-spontaneous cell death luminescence)/(maximum cell death luminescence-spontaneous cell death luminescence) ]To calculate the percentage of specific lysis.
Additional information regarding exemplary luciferase cytotoxicity assays can be found in Matta H et al, "Development and characterization of a novel luciferase based cytotoxicity assay" Scientific Reports (2018) 8,199, which is expressly incorporated herein by reference in its entirety.
Interferon-gamma assessment
In 6-well tissue culture plates, the following effectors were used: target cell ratio, 1X 10 per well stimulated with target cells 6 anti-EpCAM CAR T cells were 24 hours. Interferon gamma (IFN- γ) and IL-2 secretion were quantified by enzyme-linked immunosorbent assay (ELISA) using human IL-2ELISA kit II (BD, 550611) and human IFN- γ ELISA kit II (BD, 550612).
CD25/CD69 assay
In 6-well tissue culture plates, the following effectors were used: target cell ratio, 1X 10 per well stimulated with target cells 6 anti-EpCAM CAR T cells were 24 hours. Cells were stained with a near IR dead cell staining kit (thermosfisher) that was live/dead fixable to label dead cells and stained with anti-CD 3, and CAR-T cells were identified as cd3+gfp+ cells by flow cytometry. Staining with Alexa Fluor 700 anti-human CD69 antibody (Biolegend) and PE anti-CD 25 antibody (Biolegend) CD69 and CD25 on CAR-T cells.
Sequencing of CAR T cell libraries
Cells were collected from the anti-EpCAM CAR-T library screen. Genomic DNA (gDNA) was extracted using the blood/cell genomic DNA mini kit (Tiangen, DP 304-03). 75ng of gDNA was used in PCR to amplify the CAR region of the library. The amplified region was TA cloned and sequenced using the TA/Blunt-Zero cloning kit (Vazyme, C601).
Example 2 exemplary anti-EpCAM CAR T cell line is effective against cancer
Several anti-EpCAM CAR T cell lines were prepared from the anti-EpCAM conjugates disclosed herein. The construct is expressed in T cells isolated from a donor designated Y1342. Cytotoxicity assays were performed against SNU719 gastric cancer cells at a 1:1 effector to target ratio as described in example 1. The percent target cell lysis and interferon gamma quantification was performed (fig. 2). The anti-EpCAM CAR T cell line exhibiting 100% target cell lysis (as shown by those reaching the 100% dashed line of the marker) was selected for further characterization. For each CAR-T line construct, concomitant quantification of interferon gamma is also depicted.
An exemplary anti-EpCAM CAR T cell line B4T2-003 was tested in an in vivo NSG mouse model. In the xenograft model of cell line origin, administration of B4T2-003 resulted in significant clearance of xenografts from NCI-N87 (N87) gastric and H2110 non-small cell lung cancer tumors, whereas tumor growth in control mice progressed (fig. 3).
Tumor re-challenge studies were performed using the anti-EpCAM CAR T cell line B4T2-003, and the results are shown in fig. 4. The initial CAR T cell infusion was administered to the SNU-719 pancreatic xenograft model on day 0. Although control mice exhibited unrestricted tumor growth, mice administered B4T2-003 exhibited undetectable tumor volumes as early as day 70. Groups of these mice were re-transplanted with a second tumor. The re-transplant reached peak volume at about day 112, but was completely cleared around day 124. This suggests that B4T2-003 remains persistent for a considerable period of time and is able to drive a second complete response.
Example 3 anti-EpCAM CAR-T cells for the treatment of cancer
The patient has cancer, e.g., cancer that expresses or overexpresses EpCAM (e.g., such that EpCAM can be used as a biomarker to detect and target cancer). In some cases, the cancer is breast cancer, colorectal cancer, renal cancer, liver cancer, lung cancer, brain cancer, pancreatic cancer, bladder cancer, testicular cancer, prostate cancer, gastric cancer, ovarian cancer, head and neck cancer, gall bladder cancer, hematological malignancy, or any combination thereof. In some cases, hematological malignancies can include leukemia, acute lymphoblastic leukemia, acute myelogenous leukemia, chronic lymphocytic leukemia, hairy cell leukemia, lymphoma, hodgkin's disease, non-hodgkin's lymphoma, or multiple myeloma.
The one or more CAR T cells disclosed herein, which may include any one or more anti-EpCAM CARs and/or anti-EpCAM conjugates, are administered to a patient enterally, orally, intranasally, parenterally, intravenously, intraperitoneally, intramuscularly, intraarterially, intraventricularly, intradermally, intralesionally, intracranially, intrathecally, or subcutaneously.
Can be used as 10 per dose 4 、10 5 、10 6 、10 7 、10 8 Or 10 9 The CAR T cells are administered at a dose of the amount of the CAR T cells that is either any number of cells within the range defined by any two of the foregoing per dose of cells, or any number of cells that are effective and/or safe as determined by a trained medical practitioner. The dose is administered every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 36 or 48 days or weeks, or at any time within a range defined by any two of the foregoing times, or at any time of administration that is effective and/or safe as determined by a trained medical practitioner.
An improvement in cancer or symptoms thereof is observed in the patient after administration of one or more CAR T cells. Administration of the CAR T cells can be performed in combination with another therapy for cancer, including but not limited to immunotherapy, chemotherapy, radiation therapy, surgery, photodynamic therapy, or targeted therapy.
In at least some of the previously described embodiments, one or more elements used in one embodiment may be used interchangeably in another embodiment unless such substitution is technically not feasible. Those skilled in the art will appreciate that various other omissions, additions and modifications may be made to the methods and structures described above without departing from the scope of the claimed subject matter. All such modifications and variations are intended to fall within the scope of the subject matter defined by the appended claims.
With respect to the use of substantially any plural and/or singular terms herein, those having skill in the art can translate from the plural to the singular and/or from the singular to the plural as is appropriate to the context and/or application. For clarity, various singular/plural permutations may be explicitly set forth herein.
It will be understood by those within the art that, in general, terms used herein, especially in the appended claims (e.g., bodies of the appended claims), are generally intended as "open" terms (e.g., the term "including" should be interpreted as "including but not limited to," the term "having" should be interpreted as "having at least," the term "comprising" should be interpreted as "including but not limited to," etc.). It will be further understood by those with skill in the art that if a specific number of an introduced claim recitation is intended, such an intent will be explicitly recited in the claim, and in the absence of such recitation no such intent is present. For example, as an aid to understanding, the following appended claims may contain usage of the introductory phrases "at least one/at least one" and "one or more/one or more" to introduce claim recitations. However, the use of such phrases should not be construed to imply that the introduction of a claim recitation by the indefinite articles "a" or "an" limits any particular claim containing such introduced claim recitation to embodiments containing only one such recitation, even when the same claim includes the introductory phrases "one or more" or "at least one" and indefinite articles such as "a" or "an" (e.g., "a" and/or "an" are to be interpreted to mean "at least one" or "one or more"); the same holds true for the use of definite articles used to introduce claim recitations. In addition, even if a specific number of an introduced claim recitation is explicitly recited, those skilled in the art will recognize that such recitation should be interpreted to mean at least the recited number (e.g., the bare recitation of "two recitations," without other modifiers, means at least two recitations, or two or more recitations). Furthermore, in those instances where a convention analogous to "at least one of A, B and C, etc." is used, such a construction in general is intended in the sense one having skill in the art would understand the convention (e.g., "a system having at least one of A, B and C" would include but not be limited to systems having a alone, B alone, C, A and B together alone, a and C together, B and C together, and/or A, B and C together, etc.). In those instances where a convention analogous to "at least one of A, B or C, etc." is used, such a construction in general is intended in the sense one having skill in the art would understand the convention (e.g., "a system having at least one of A, B or C" would include but not be limited to systems having a alone, B alone, C, A and B together, a and C together, B and C together, and/or A, B and C together, etc.). Those skilled in the art will further appreciate that virtually any discrete (or discrete) word and/or phrase presenting two or more alternative terms, whether in the specification, claims, or drawings, should be understood to contemplate the possibilities of including one of the terms, either of the terms, or both terms. For example, the phrase "a or B" will be understood to include the possibilities of "a" or "B" or "a and B".
In addition, where features or aspects of the disclosure are described in terms of markush groups, those skilled in the art will recognize that the disclosure is also thereby described in terms of any individual member or subgroup of members of the markush group.
As will be understood by those of skill in the art, for any and all purposes, as for providing a written description, all ranges disclosed herein also encompass any and all possible subranges and combinations of subranges thereof. Any listed range can be readily considered as sufficiently descriptive and so that the same range can be broken down into at least equal halves, thirds, quarters, fifths, tenths, etc. As non-limiting examples, each range discussed herein can be readily divided into a lower third, a middle third, an upper third, and the like. As will also be understood by those skilled in the art, all language such as "at most", "at least", "greater than", "less than" and the like include the recited numbers and refer to ranges that may be subsequently divided into sub-ranges as discussed above. Finally, as will be appreciated by those skilled in the art, a range includes each individual member. Thus, for example, a group of 1-3 items refers to a group of 1, 2, or 3 items. Similarly, a group of 1-5 items refers to a group of 1, 2, 3, 4, or 5 items, and so forth.
While various aspects and embodiments have been disclosed herein, other aspects and embodiments will be apparent to those skilled in the art. The various aspects and embodiments disclosed herein are for purposes of illustration and are not intended to be limiting, with the true scope and spirit being indicated by the following claims.
All references cited herein, including but not limited to published and unpublished applications, patents and references, are incorporated herein by reference in their entirety and thereby form a part of this specification. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in this specification, this specification is intended to supersede and/or take precedence over any such contradictory material.
Sequence listing
EpCAMSequence(s)
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Sequence listing
<110> Boaoadisi biotechnology company (BioArdis, LLC)
<120> EPCAM binding molecules and uses thereof
<130> BWGB.007WO
<150> US 63/127885
<151> 2020-12-18
<150> US 63/262310
<151> 2021-10-08
<160> 52
<170> PatentIn version 3.5
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Gly Ser Thr Ser Ser Phe Asn Tyr
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Gly Phe Thr Phe Arg His Asp Val
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Gly Tyr Thr Phe Ser Phe Asp Phe
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Gly Arg Thr Phe Ser Tyr Asn Pro
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Gly Ser Ile Tyr Asn Phe Asp Tyr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ile Ser Arg Thr Gly Gly Ser Thr
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Ala Arg Gly Lys Thr Gln Leu Ala Trp Gln Gln Ala Pro Asp Ser Leu
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Thr Val Phe Gly Tyr
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Ala Thr Tyr Tyr Trp Pro Thr Glu Gly Asp Tyr Ser Tyr
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Ala Arg Gln Phe Leu Asn His Pro Thr Ala Leu Gly Tyr
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Ala Ala Gly Val Arg Ala Glu Asp Gly Arg Val Arg Thr Leu Pro Ser
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Ala Arg Gln Leu Gly Ala Gln Gly Glu Pro Asn Val Ser Leu Gly Tyr
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Ala Arg Gln Lys Lys Gln Met Gly Arg Met Asp Gly Gln Ala Phe Gln
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His Asp Tyr
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Ala Arg Asp Glu Arg Thr Thr Arg Ile Gly Leu Gly Tyr
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Val Arg Ala Asn Phe Leu Asn Ser His Ala Leu Gly Tyr
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Ala Arg His Leu His Ala Pro Ser Val Gly Arg Ala Asp Gly Tyr Gly
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His Gly Tyr
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Ala Arg Leu Arg Gly Glu Phe Pro Asn Ala Phe Gly Tyr
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Ala Arg Gln Lys Asp Gln Gly Gln Val Ile His Gly Tyr
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Val Arg Thr Ser Val Asp Arg Val Thr Asn Ile Glu Pro Phe Ser Tyr
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<223> EPCAM-B-F02 HCDR3
<400> 39
Ala Arg Gln Ser Ala Arg Ala Asn Leu Ala Leu Gly Tyr
1 5 10
<210> 40
<211> 129
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-A-B01 VH
<400> 40
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Tyr Thr Phe Gly Ile Asp
20 25 30
Phe Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Ala Arg Gly Lys Thr Gln Leu Ala Trp Gln Gln Ala Pro Asp Ser
100 105 110
Leu Thr Val Phe Gly Tyr Trp Gly Gln Gly Thr Gln Val Thr Val Ser
115 120 125
Ser
<210> 41
<211> 121
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-A-C01 VH
<400> 41
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Phe Ile Ser Arg Leu Tyr
20 25 30
His Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Ala Thr Tyr Tyr Trp Pro Thr Glu Gly Asp Tyr Ser Tyr Trp Gly
100 105 110
Gln Gly Thr Gln Val Thr Val Ser Ser
115 120
<210> 42
<211> 121
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-A-E01 VH
<400> 42
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Ser Ile Tyr Ser Val Asp
20 25 30
Phe Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Ala Arg Gln Phe Leu Asn His Pro Thr Ala Leu Gly Tyr Trp Gly
100 105 110
Gln Gly Thr Gln Val Thr Val Ser Ser
115 120
<210> 43
<211> 128
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-A-B02 VH
<400> 43
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Tyr Thr Phe Ser Ser Tyr
20 25 30
Val Met Arg Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Ala Ala Gly Val Arg Ala Glu Asp Gly Arg Val Arg Thr Leu Pro
100 105 110
Ser Glu Tyr Thr Phe Trp Gly Gln Gly Thr Gln Val Thr Val Ser Ser
115 120 125
<210> 44
<211> 124
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-A-C02 VH
<400> 44
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Ser Thr Tyr Asn Val Tyr
20 25 30
Val Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Ala Arg Gln Leu Gly Ala Gln Gly Glu Pro Asn Val Ser Leu Gly
100 105 110
Tyr Trp Gly Gln Gly Thr Gln Val Thr Val Ser Ser
115 120
<210> 45
<211> 127
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-A-D02 VH
<400> 45
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Gly Thr Phe Ser Tyr Asp
20 25 30
Phe Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Ala Arg Gln Lys Lys Gln Met Gly Arg Met Asp Gly Gln Ala Phe
100 105 110
Gln His Asp Tyr Trp Gly Gln Gly Thr Gln Val Thr Val Ser Ser
115 120 125
<210> 46
<211> 121
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-A-A03 VH
<400> 46
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Ser Ile Ser Asn Val Tyr
20 25 30
Ile Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Ala Arg Asp Glu Arg Thr Thr Arg Ile Gly Leu Gly Tyr Trp Gly
100 105 110
Gln Gly Thr Gln Val Thr Val Ser Ser
115 120
<210> 47
<211> 121
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-A-B03 VH
<400> 47
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Ser Thr Ser Ser Phe Asn
20 25 30
Tyr Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Val Arg Ala Asn Phe Leu Asn Ser His Ala Leu Gly Tyr Trp Gly
100 105 110
Gln Gly Thr Gln Val Thr Val Ser Ser
115 120
<210> 48
<211> 127
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-B-B01 VH
<400> 48
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Phe Thr Phe Arg His Asp
20 25 30
Val Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Ala Arg His Leu His Ala Pro Ser Val Gly Arg Ala Asp Gly Tyr
100 105 110
Gly His Gly Tyr Trp Gly Gln Gly Thr Gln Val Thr Val Ser Ser
115 120 125
<210> 49
<211> 121
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-B-D01 VH
<400> 49
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Tyr Thr Phe Ser Phe Asp
20 25 30
Phe Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Ala Arg Leu Arg Gly Glu Phe Pro Asn Ala Phe Gly Tyr Trp Gly
100 105 110
Gln Gly Thr Gln Val Thr Val Ser Ser
115 120
<210> 50
<211> 121
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-B-F01 VH
<400> 50
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Ser Thr Phe Ser Phe Asn
20 25 30
Phe Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Ala Arg Gln Lys Asp Gln Gly Gln Val Ile His Gly Tyr Trp Gly
100 105 110
Gln Gly Thr Gln Val Thr Val Ser Ser
115 120
<210> 51
<211> 124
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-B-B02 VH
<400> 51
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Arg Thr Phe Ser Tyr Asn
20 25 30
Pro Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Val Arg Thr Ser Val Asp Arg Val Thr Asn Ile Glu Pro Phe Ser
100 105 110
Tyr Trp Gly Gln Gly Thr Gln Val Thr Val Ser Ser
115 120
<210> 52
<211> 121
<212> PRT
<213> Artificial sequence (Artificial Sequence)
<220>
<223> EPCAM-B-F02 VH
<400> 52
Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15
Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Ser Ile Tyr Asn Phe Asp
20 25 30
Tyr Met Gly Trp Phe Arg Gln Ala Pro Gly Lys Gly Arg Glu Leu Val
35 40 45
Ala Ala Ile Ser Arg Thr Gly Gly Ser Thr Tyr Tyr Pro Asp Ser Val
50 55 60
Glu Gly Arg Phe Thr Ile Ser Arg Asp Asn Ala Lys Arg Met Val Tyr
65 70 75 80
Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95
Ala Ala Arg Gln Ser Ala Arg Ala Asn Leu Ala Leu Gly Tyr Trp Gly
100 105 110
Gln Gly Thr Gln Val Thr Val Ser Ser
115 120

Claims (22)

1. An epithelial cell adhesion molecule (EpCAM) binding polypeptide comprising an immunoglobulin heavy chain variable domain comprising a CDR-H1, a CDR-H2, and a CDR-H3, wherein:
The CDR-H1 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOs 1-13;
the CDR-H2 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOs 14-26; and is also provided with
The CDR-H3 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from SEQ ID NOS 27-39.
2. The EpCAM binding polypeptide of claim 1, wherein:
1) The CDR-H1 comprises the sequence of SEQ ID NO. 1, the CDR-H2 comprises the sequence of SEQ ID NO. 14, and the CDR-H3 comprises the sequence of SEQ ID NO. 27;
2) The CDR-H1 comprises the sequence of SEQ ID NO. 2, the CDR-H2 comprises the sequence of SEQ ID NO. 15, and the CDR-H3 comprises the sequence of SEQ ID NO. 28;
3) The CDR-H1 comprises the sequence of SEQ ID NO. 3, the CDR-H2 comprises the sequence of SEQ ID NO. 16, and the CDR-H3 comprises the sequence of SEQ ID NO. 29;
4) The CDR-H1 comprises the sequence of SEQ ID NO. 4, the CDR-H2 comprises the sequence of SEQ ID NO. 17, and the CDR-H3 comprises the sequence of SEQ ID NO. 30;
5) The CDR-H1 comprises the sequence of SEQ ID NO. 5, the CDR-H2 comprises the sequence of SEQ ID NO. 18, and the CDR-H3 comprises the sequence of SEQ ID NO. 31;
6) The CDR-H1 comprises the sequence of SEQ ID NO. 6, the CDR-H2 comprises the sequence of SEQ ID NO. 19, and the CDR-H3 comprises the sequence of SEQ ID NO. 32;
7) The CDR-H1 comprises the sequence of SEQ ID NO. 7, the CDR-H2 comprises the sequence of SEQ ID NO. 20, and the CDR-H3 comprises the sequence of SEQ ID NO. 33;
8) The CDR-H1 comprises the sequence of SEQ ID NO. 8, the CDR-H2 comprises the sequence of SEQ ID NO. 21, and the CDR-H3 comprises the sequence of SEQ ID NO. 34;
9) The CDR-H1 comprises the sequence of SEQ ID NO. 9, the CDR-H2 comprises the sequence of SEQ ID NO. 22, and the CDR-H3 comprises the sequence of SEQ ID NO. 35;
10 The CDR-H1 comprising the sequence of SEQ ID NO. 10, the CDR-H2 comprising the sequence of SEQ ID NO. 23, and the CDR-H3 comprising the sequence of SEQ ID NO. 36;
11 The CDR-H1 comprising the sequence of SEQ ID NO. 11, the CDR-H2 comprising the sequence of SEQ ID NO. 24, and the CDR-H3 comprising the sequence of SEQ ID NO. 37;
12 The CDR-H1 comprising the sequence of SEQ ID NO. 12, the CDR-H2 comprising the sequence of SEQ ID NO. 25 and the CDR-H3 comprising the sequence of SEQ ID NO. 38; or alternatively
13 The CDR-H1 comprising the sequence of SEQ ID NO:13, the CDR-H2 comprising the sequence of SEQ ID NO:26, and the CDR-H3 comprising the sequence of SEQ ID NO: 39.
3. The EpCAM binding polypeptide of claim 1 or 2 wherein said heavy chain variable domain comprises an amino acid sequence having at least 90%, 95%, 99% or 100% sequence identity to any sequence selected from SEQ ID NOs 40 to 52.
An epcam binding polypeptide comprising an immunoglobulin heavy chain variable domain comprising a CDR-H2, wherein said CDR-H2 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOs 14-26.
5. The EpCAM binding polypeptide of claim 4 wherein said immunoglobulin heavy chain variable domain further comprises a CDR-H1, wherein said CDR-H1 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOs 1-13.
6. The EpCAM binding polypeptide of claim 4 or 5 wherein said immunoglobulin heavy chain variable domain further comprises a CDR-H3, wherein said CDR-H3 comprises a sequence having at least 90%, 95%, 99% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOs 27 to 39.
7. The EpCAM binding polypeptide of any one of claims 1 to 6 wherein said EpCAM binding polypeptide is humanized.
8. The EpCAM binding polypeptide of any one of claims 1 to 7 wherein said EpCAM binding polypeptide is a single domain antibody (sdAb).
9. A Chimeric Antigen Receptor (CAR) comprising the EpCAM binding polypeptide of any one of claims 1 to 8.
10. A Chimeric Antigen Receptor (CAR) cell comprising the CAR of claim 9.
11. The CAR cell of claim 10, wherein the CAR cell is a CAR T cell.
12. The CAR cell of claim 10 or 11, wherein the CAR cell comprises at least two binding polypeptides and the CAR cell is a multivalent CAR cell.
13. The CAR cell of any one of claims 10-12, wherein the CAR cell is derived from a subject or cell line.
14. The CAR cell of claim 13, wherein the subject has cancer.
15. The CAR cell of claim 14, wherein the cancer is breast cancer, colorectal cancer, kidney cancer, liver cancer, lung cancer, brain cancer, pancreatic cancer, bladder cancer, testicular cancer, prostate cancer, gastric cancer, ovarian cancer, head and neck cancer, gall bladder cancer, hematological malignancy, or any combination thereof.
16. A nucleic acid encoding a polypeptide comprising a sequence having at least 90%, 95%, 99% or 100% sequence identity to the EpCAM binding polypeptide of any one of claims 1 to 8 or the CAR of claim 9.
17. A method of treating cancer in a subject in need thereof, comprising administering the CAR cell of any one of claims 10-15.
18. The method of claim 17, wherein the chimeric antigen receptor cells are autologous or allogeneic to the subject.
19. The method of claim 17 or 18, wherein the subject is a mammal.
20. The method of any one of claims 17-19, wherein the subject is a human.
21. The method of any one of claims 17-20, wherein the cancer is breast cancer, colorectal cancer, renal cancer, liver cancer, lung cancer, brain cancer, pancreatic cancer, bladder cancer, testicular cancer, prostate cancer, gastric cancer, ovarian cancer, head and neck cancer, gall bladder cancer, hematological malignancy, or any combination thereof.
22. The method of any one of claims 17-21, wherein the chimeric antigen receptor cells are administered parenterally.
CN202180093995.9A 2020-12-18 2021-12-16 EPCAM binding molecules and uses thereof Pending CN117279937A (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US63/127,885 2020-12-18
US202163262310P 2021-10-08 2021-10-08
US63/262,310 2021-10-08
PCT/US2021/063847 WO2022133110A1 (en) 2020-12-18 2021-12-16 Epcam binding molecules and uses thereof

Publications (1)

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CN117279937A true CN117279937A (en) 2023-12-22

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