JP2020141702A - Glypican epitopes and uses thereof - Google Patents

Abstract

To solve the problem in which: in view of the association between GPC-1 levels and prostate cancer, a need exists for the identification of epitopes within GPC-1 that are advantageous for detecting and quantifying GPC-1 levels in subjects undergoing diagnostic assays and/or prognostic tests.SOLUTION: The present inventors have determined that a series of epitopes within the GPC-1 protein are preferably targeted by binding entities including, but not limited to, antibodies.SELECTED DRAWING: Figure 1

Description

The present invention generally relates to the fields of immunology and medicine. More specifically, the present invention relates to an epitope of glypican-1 (GPC-1) and its use.

Prostate cancer is the most common cancer in men of all races, with whites, blacks, Native Americans / Alaskans, and Hispanic men having the second highest mortality rate after lung cancer. In the United States, 209,292 men were diagnosed with prostate cancer in 2011, of which 27,970 died of prostate cancer (US Cancer Working Group, United States Cancer Statists: 1999-2011 Incidence and Mortality Web-based Report, Atlanta (GA): US Department of Health and Human Services, US Center for Disease Control and Prevention, and US National Cancer Institute; 2014).

If the diagnosis of prostate cancer is early, surgery and / or radiation therapy will be effective in many patients. However, many patients with advanced cancer, as well as a significant proportion of all prostate cancer patients, will eventually develop metastatic cancer, even with topical treatment.

For this reason, there is a need for a simple, reliable, and highly accurate test method for diagnosing prostate cancer, especially in the early stages.

Glypican-1 (GPC-1) is one of the cell surface heparan sulfate proteoglycans and has a core protein bound to the cell membrane via glycosylphosphatidylinositol. GPC-1 is a member of the large Gripican family. GPC-1 has been reported to be overexpressed in some forms of cancer (eg, pancreatic cancer, breast cancer), but expression is not significantly different from other cancers. We have recently shown that GPC-1 is overexpressed by prostate cancer cells and can be used as a means of diagnosing prostate cancer (Walsh et al., "Cell Surface Prostate Cancer Antigen for Diagnosis". US Patent Provisional Application No. 61/928/776 (unpublished); Walsh et al., International Application PCT / AU2014 / 00999, "Monoclonal Anti-GPC-1 Antibodies and uses theeof" (unpublished)).

Given the relationship between GPC-1 levels and prostate cancer revealed by us, it is advantageous to detect and quantify GPC-1 levels in patients undergoing diagnostic assays and / or prognostic tests. It is necessary to identify the epitope in GPC-1.

We have shown that a series of epitopes within the GPC-1 protein are preferred to be targeted by binding entities, including but not particularly limited.

Therefore, the present invention relates to at least the following embodiments:

Embodiment 1:
An epitope of an anti-glypican 1 (GPC-1) antibody located within a portion of the GPC-1 mobile loop defined by the amino acid sequence KVNPQGPPGPEEK (SEQ ID NO: 1).

Embodiment 2:
(I) VNPQGPPGPEEK (SEQ ID NO: 2); or (ii) a variant of VNPQGPPGPEEK (SEQ ID NO: 2).
One or more of the 2nd, 3rd, 7th, 8th, 9th, 10th and / or 11th positions; or 1st, 2nd, 3rd, 4th, 6th, One or more of the 8th, 10th and / or 11th positions; or the 1st, 2nd, 3rd, 4th, 5th, 8th, 10th and / or 11th positions The epitope of Embodiment 1, comprising a first segment comprising an amino acid sequence selected from a variant comprising a substituted amino acid residue only at any one or more positions of.

Embodiment 3:
(I) KVNPQGPGP (SEQ ID NO: 6); or (ii) KVNPQGPGP (SEQ ID NO: 6) substituted amino acids only at one or more of the 1st, 3rd, 4th, 8th and 9th positions. The epitope according to embodiment 1, comprising a first segment comprising an amino acid sequence selected from the variant of SEQ ID NO: 6, comprising a residue.

Embodiment 4:
The variant according to embodiment 3, which comprises a substituted amino acid residue only at one or more of positions 8 and 9 of SEQ ID NO: 6.

Embodiment 5:
(I) KVNPQGPGPE (SEQ ID NO: 5); or (ii) KVNPQGPPGPE (SEQ ID NO: 5) at one or more of the 1st, 3rd, 4th, 8th, 9th and 10th positions. The epitope according to embodiment 1, comprising a first segment comprising an amino acid sequence selected from the variant of SEQ ID NO: 5, containing only a substituted amino acid residue.

Embodiment 6:
The variant according to embodiment 5, which comprises a substituted amino acid residue only at one or more of positions 8, 9, and 10 of SEQ ID NO: 6.

Embodiment 7:
The variant according to embodiment 5 or 6, wherein the E (glu) at position 10 is replaced with any other amino acid.

Embodiment 8:
1st place where K (lys) is replaced with any one of W (trp), R (arg), L (lys), Y (tyr) or F (phe);
The third position where N (asn) is replaced with any one of H (his), P (pro) or D (asp);
4th place where P (pro) is replaced by any one of R (arg), K (lys), W (trp), S (ser), H (his) or N (asn);
G (gly) is replaced with any one of D (asp), E (glu), N (asn), Q (gln), K (lys), R (arg) or A (ala) 8 Rank;
P (pro) is M (met), A (ala), I (ile), K (lys), R (arg), Q (grn), S (ser), T (thr) or Y (tyr). The variant according to any one of embodiments 3-7, wherein the variant comprises substitution only at any one or more positions of the 9-position substituted with any one.

Embodiment 9:
The epitope of any one of embodiments 1-8, comprising a second segment comprising the amino acid sequence TQNARA (SEQ ID NO: 8).

Embodiment 10:
The epitope according to any one of embodiments 1-8, comprising a second segment comprising the amino acid sequence TQNARAFRD (SEQ ID NO: 7).

Embodiment 11:
(I) NPQGPPGPEE (SEQ ID NO: 4); or (ii) at one or more of the 1st, 2nd, 3rd, 5th, 7th and 9th positions of NPQGPGPEE (SEQ ID NO: 4). The epitope according to embodiment 1 or 2, comprising a first segment comprising an amino acid sequence selected from the variant of SEQ ID NO: 4, which comprises only a substituted amino acid residue.

Embodiment 12:
The variant according to embodiment 11, wherein the variant comprises a substituted amino acid residue only at any one or more of positions 2, 7, and 9 of SEQ ID NO: 4.

Embodiment 13:
1st place where N (asn) is replaced by H (his);
2nd position where P (pro) is replaced with any other amino acid;
The third position where Q (gln) is replaced with any one of N (asn), M (met), T (thr), S (ser) or R (arg);
5th place where P (pro) is replaced by A (ala);
P (pro) is A (ala), D (asp), C (cys), E (glu), Z (glx), G (gly), H (his), K (lys), M (met), 7th position substituted with any one of F (phe), P (pro), S (ser), T (thr), W (trp) or Y (tyr);
The variant according to embodiment 11 or 12, wherein E (glu) comprises a substitution at any one or more positions of the 9-position substituted with any other amino acid.

Embodiment 14:
The epitope according to any one of embodiments 11 to 13, comprising a second segment comprising the amino acid sequence ALSTASDDR (SEQ ID NO: 9).

Embodiment 15:
(I) VNPQGPGPEE (SEQ ID NO: 3); or (ii) one or more of VNPQGPGPEE (SEQ ID NO: 3) 1st, 2nd, 3rd, 4th, 5th, 8th and 10th. The epitope according to embodiment 1 or 2, comprising a first segment comprising an amino acid sequence selected from the variant of SEQ ID NO: 3, which comprises a substituted amino acid residue only at position.

Embodiment 16:
The variant according to embodiment 15, wherein the variant comprises a substituted amino acid residue only at any one or more of positions 1, 2, 3, and 8 of SEQ ID NO: 3.

Embodiment 17:
Position 1 where V (val) is replaced with any other amino acid;
2nd position where N (asn) is replaced with any other amino acid;
Position 3 where P (pro) is replaced with any other amino acid;
Q (gln) is Y (tyr), A (ala), E (glu), V (val), M (met), F (phe), L (leu), I (ile), T (thr) or 4th place replaced by any one of R (arg);
G (glyc) is any one of A (ala), S (ser), T (thr), H (his), W (trp), Y (tyr), F (phe) or M (met). Substituted 5th place;
Position 8 where P (pro) is replaced with any other amino acid;
Replace at one or more of the 10 positions where E (glu) is replaced with Q (gln), D (asp), F (phe), H (his) or M (met). 25. The variant according to embodiment 15 or 16.

Embodiment 18:
Amino acid sequence PERRPP (SEQ ID NO: 10) or amino acid sequence QDASSDDGSGS (SEQ ID NO: 11)
The epitope according to any one of embodiments 15 to 17, comprising a second segment comprising.

Embodiment 19:
The epitope of any one of embodiments 15-17, comprising a second segment comprising the amino acid sequence PERRPP (SEQ ID NO: 10) and a third segment comprising the amino acid sequence QDASDDGSGS (SEQ ID NO: 11).

Embodiment 20:
The epitope according to any one of embodiments 1 to 10, comprising the amino acid sequence CGELYTQNARAFRDLCGNPKVNPQGPPGPEEKRRRGC (SEQ ID NO: 12).

Embodiment 21:
The epitope according to any one of embodiments 1 to 20, which is a linear epitope.

Embodiment 22:
The epitope according to embodiment 19, wherein the second segment and the third segment of the epitope are discontinuous.

Embodiment 23:
The epitope according to any one of embodiments 9, 10, 14, 18 or 22, wherein the first segment and the second segment of the epitope are discontinuous.

Embodiment 24:
Select from one or more of TQNARA (SEQ ID NO: 8), ALSTASDDR (SEQ ID NO: 9), PSERPP (SEQ ID NO: 10), QDASDDGSGS (SEQ ID NO: 11), LGPECSRAVMK (SEQ ID NO: 13) and TQNARAFRD (SEQ ID NO: 7). An epitope of an anti-glypican 1 (GPC-1) antibody comprising the amino acid sequence to be used.

Embodiment 25:
The epitope according to any one of embodiments 1 to 24, which is an isolated polypeptide or a synthetic polypeptide.

Embodiment 26:
Contains a combination of two or more different epitopes
Whether the different epitopes are the epitopes according to any one of embodiments 1 to 25;
Are each of the epitopes listed in Table 1;
The combination of the epitopes is any one or more combinations shown in Table 3.
Assortment of epitopes.

Embodiment 27:
Contains a combination of two or more different epitopes
The first epitope according to any one of embodiments 1 to 10 and
The second epitope according to any one of embodiments 11 to 14 and the like.
Assortment of epitopes.

Embodiment 28:
Contains a combination of two or more different epitopes
The first epitope according to any one of embodiments 1 to 10 and
Containing with a second epitope according to any one of embodiments 15-19,
Assortment of epitopes.

Embodiment 29:
A composition comprising an epitope according to any one of embodiments 1-25 or an combination of the epitope according to any one of embodiments 26-28 and a pharmaceutically acceptable carrier or excipient. ..

Embodiment 30:
An assembly comprising an epitope according to any one of embodiments 1 to 25 or an epitope according to any one of embodiments 26 to 28 attached to one or more soluble or insoluble supports. body.

Embodiment 31:
The aggregate according to embodiment 30, which is a component of an enzyme-linked immunosorbent assay (ELISA).

Embodiment 32:
A nucleic acid encoding the epitope according to any one of embodiments 1-25.

Embodiment 33:
A vector containing the nucleic acid according to embodiment 32.

Embodiment 34:
A host cell comprising the vector according to embodiment 33.

Embodiment 35:
An isolated binding entity capable of specifically binding to the epitope according to any one of embodiments 1 to 25, which is not an antibody.

Embodiment 36:
An isolated binding entity capable of specifically binding to the epitope according to any one of embodiments 1-25, which is an antibody, wherein the antibody is a MIL38 antibody (CBA20140026), rabbit anti-antibody. A binding entity that is not a GPC-1 polyclonal antibody (ab137604, abcam), a mouse anti-glypican monoclonal antibody 2600 clone 4D1 (Millipore) or a goat anti-glypican 1 antibody (AA24-530).

Embodiment 37:
A method for detecting prostate cancer of a subject, that is, collecting a biological sample from the subject, detecting the presence of the epitope according to any one of Embodiments 1 to 25 in the sample, and in the sample. A method comprising determining whether a subject has or is likely to develop prostate cancer based on the amount of epitopes detected.
The biological sample can be a body fluid sample.
The biological sample can be a tissue sample.

Embodiment 38:
Detecting the presence of an epitope in a sample comprises contacting the sample with a binding entity capable of specifically binding to the epitope according to any one of embodiments 1-25. The method according to form 37.

Embodiment 39:
38. The method of embodiment 38, wherein the binding entity is a population of antibodies.

Embodiment 40:
The antibody population is MIL38 antibody (CBA20140026), rabbit anti-GPC-1 polyclonal antibody (ab137604, abcam), mouse anti-glypican monoclonal antibody 2600 clone 4D1 (Millipore) or goat anti-glypican 1 antibody (AA24-530). 39. The method of embodiment 39, comprising any one or more.

Embodiment 41:
The antibody population is MIL38 antibody (CBA20140026), rabbit anti-GPC-1 polyclonal antibody (ab137604, abcam), mouse anti-glypican monoclonal antibody 2600 clone 4D1 (Millipore) or goat anti-glypican 1 antibody (AA24-530). The method according to embodiment 39, which does not include any of them.

Embodiment 42:
When it is detected that the amount of epitopes in the body fluid sample is greater than the same measurement in the control sample, including comparing the amount of epitopes present in the biological sample with the amount of epitopes present in the control sample. , The method of any one of embodiments 37-41, which indicates that the subject has prostate cancer or is likely to develop prostate cancer in the subject.

Embodiment 43:
42. The method of embodiment 42, wherein the amount of epitopes detected in the sample is more than 50% greater than the amount of epitopes detected in the control sample.

Embodiment 44:
The method of any one of embodiments 37-43, wherein detecting the presence of an epitope comprises contacting the sample with a population of MIL38 antibodies deposited with Cellbank Australia under accession number CBA20140026. ..

Embodiment 45:
Detecting the presence of an epitope contains or comprises the sample and the amino acid sequences defined by positions 48-58 of SEQ ID NO: 20 Complementarity determining regions 1 (CDR1); positions 74-80 of SEQ ID NO: 20. Complementarity determining regions 2 (CDR2) comprising or consisting of amino acid sequences defined by; and / or complementarity determining regions 3 (CDR3) comprising or consisting of amino acid sequences defined by positions 113-121 of SEQ ID NO: 20. The method of any one of embodiments 37-43, comprising contacting with a population of antibodies that does not contain antibodies that include light chain variable regions comprising.

Embodiment 46:
The method of any one of embodiments 37-45, further comprising determining the level of prostate-specific antigen (PSA) in a biological sample and comparing the detected level with that of a control sample. ..

Embodiment 47:
The method according to any one of embodiments 37 to 46, wherein the biological sample is a body fluid sample.

Embodiment 48:
The method according to any one of embodiments 37 to 46, wherein the biological sample is a tissue sample.

Embodiment 49:
A fusion protein comprising the epitope according to any one of embodiments 1-25.

Embodiment 50:
The epitope according to any one of embodiments 1 to 25, the combination of the epitopes according to any one of embodiments 26 to 28, or the combination of epitopes according to embodiment 48 as a positive control element of the method for detecting GPC-1. Use of fusion proteins.

Embodiment 51:
The use according to embodiment 50, wherein the method is the method for detecting prostate cancer according to any one of embodiments 37-48.

Positive control elements used in a detection method or assay generate positive / positive signals directly or indirectly so that the method or assay can function correctly, at least in part or in whole. Can be confirmed.

From this, a preferred embodiment of the present invention will be described with reference to the accompanying drawings as a mere example.

It is a rendered image of the chain B existing as Protein Data Bank identification number (PBD ID) 4AD7 (http://www.ebi.ac.uk/pdbsum/4AD7). It is a graph of the box plot of the unprocessed data of MIL38-AM4 antibody screening. The bottom and top edges of the box are the first and third quartiles of the data. The band near the center of the box is the second quartile (median). The whiskers are 1.5 times the interquartile range and show statistical outliers in the dataset (Mcgill et al., The American Statician, 32: 12-16, 1978). A plot of peptide numbers against intensities recorded by incubating all five arrays (sets 1-5 of Example 1) with 1 μg / ml (upper trace) or 10 μg / ml (lower trace) MIL38-AM4. .. The sequence TQNARAFRDLYS (SEQ ID NO: 21) is represented by a dark sphere and the residues K347, V348, G362 and K363 are represented by a light sphere Protein Data Bank Identification Number (PBD ID) 4AD7 (http://www.ebi. It is a rendered image of the chain B of ac.uk / pdbsum / 4AD7). In X-ray diffraction, the loop connecting V348 and G362 is not resolved. FIG. 6 is a boxplot graph of unprocessed data for screening for polyclonal and monoclonal anti-GPC-1 and MIL38-AM3 antibodies. The bottom and top edges of the box are the first and third quartiles of the data. The band near the center of the box is the second quartile (median). The whiskers are 1.5 times the interquartile range and show statistical outliers in the dataset (Mcgill et al., The American Statician, 32: 12-16, 1978). Plots of peptide numbers against intensities recorded by testing three commercially available anti-glypican 1 preparations on the array used for MIL38-AM4 mapping are shown for comparison. It is a rendered image of the chain B of the Protein Data Bank identification number (PBD ID) 4AD7 (http://www.ebi.ac.uk/pdbsum/4AD7). FIG. 7A is a rendered image of chain B in which the sequence PERRPP (SEQ ID NO: 10) is represented by a light colored sphere and the residues K347, V348, G362 and K363 are represented by a dark sphere. In X-ray diffraction, the loop connecting V348 and G362 is not resolved. These epitopes are recognized by rabbit anti-GPC-1. The additional epitope QDASDDGSGS (SEQ ID NO: 11) is not resolved in the coordinate file. FIG. 7B is a rendered image of chain B in which the sequence LGPECSRAVMK (SEQ ID NO: 13) is represented by a shaded sphere. This epitope is recognized by mouse anti-GPC-1. It is a graph of the box-whisker plot of the unprocessed data of antibody screening. The bottom and top edges of the box are the first and third quartiles of the data. The band near the center of the box is the second quartile (median). The whiskers are 1.5 times the interquartile range and show statistical outliers in the dataset (Mcgill et al., The American Statician, 32: 12-16, 1978). It is a figure which represented the rabbit polyclonalAb137604 probed by the substitution analysis of a set 3 in a letter plot. The central horizontal bar represents the average intensity recorded in the base sequence. The individual mutations are shown in the column corresponding to the location of the mutation, and the symbols are plotted at the height corresponding to the recorded intensity. It is a figure which represented the goat polyclonal anti-GPC-1 probed by the substitution analysis of set 2 (Example 3) by the letter plot. It is a figure which represented the MIL38-AM4 probed by the substitution analysis of a set 3 (Example 3) by a letter plot. It is a figure which represented the data obtained by probing MIL38-AM4 with the peptide of set 1 (Example 3) by the heat map. Signal intensities range from black (baseline) to white (mean) to gray (maximum); "X" = x-axis; the peptide sequences shown in x-axis columns X1-X33 are: The X-1 peptide is residues 344-353 of SEQ ID NO: 1; the X-2 peptide is residues 348-357 of SEQ ID NO: 1; the X-3 peptide is residues 352-361 of SEQ ID NO: 1. The X-4 peptide is residues 356-365 of SEQ ID NO: 1; the X-5 peptide is residues 344-354 of SEQ ID NO: 1; the X-6 peptide is residues 348-358 of SEQ ID NO: 1. Yes; the X-7 peptide is residues 352-362 of SEQ ID NO: 1; the X-8 peptide is residues 356-366 of SEQ ID NO: 1; the X-9 peptide is residues 344-355 of SEQ ID NO: 1. The X-10 peptide is residues 348-359 of SEQ ID NO: 1; the X-11 peptide is residues 352-363 of SEQ ID NO: 1; the X-12 peptide is residues 344-359 of SEQ ID NO: 1. 356; the X-13 peptide is residues 348-360 of SEQ ID NO: 1; the X-14 peptide is residues 352-364 of SEQ ID NO: 1; the X-15 peptide is residues 344 of SEQ ID NO: 1. ~ 357; the X-16 peptide is residues 348-361 of SEQ ID NO: 1; the X-17 peptide is residues 352-365 of SEQ ID NO: 1; the X-18 peptide is residues of SEQ ID NO: 1. 344 to 358; the X-19 peptide is residues 348 to 362 of SEQ ID NO: 1; the X-20 peptide is residues 352 to 366 of SEQ ID NO: 1; the X-21 peptide is the residue of SEQ ID NO: 1. The groups are 344 to 359; the X-22 peptide is residues 348 to 363 of SEQ ID NO: 1; the X-23 peptide is residues 344 to 360 of SEQ ID NO: 1; the X-24 peptide is residues 344 to 360 of SEQ ID NO: 1. Residues 348-364; X-25 peptide is residues 344-361 of SEQ ID NO: 1; X-26 peptide is residues 348-365 of SEQ ID NO: 1; X-27 peptide is SEQ ID NO: 1 Residues 344 to 362; the X-28 peptide is residues 348 to 366 of SEQ ID NO: 1; the X-29 peptide is residues 344 to 363 of SEQ ID NO: 1; the X-30 peptide is SEQ ID NO: 1. 1 residues 344 to 364; the X-31 peptide is residues 344 to 365 of SEQ ID NO: 1; the X-32 peptide is residues 344 to 366 of SEQ ID NO: 1; the X-33 peptide is scrambled. / Random array; "Y" = y-axis The peptide sequences shown in columns Y1 to Y19 on the y-axis are as follows: the Y-1 peptide is residues 131-140 of SEQ ID NO: 1; the Y-2 peptide is a residue of SEQ ID NO: 1. 135-144; Y-3 peptide is residues 139-148 of SEQ ID NO: 1; Y-4 peptide is residues 131-141 of SEQ ID NO: 1; Y-5 peptide is residue of SEQ ID NO: 1. The groups are 135-145; the Y-6 peptide is residues 139-149 of SEQ ID NO: 1; the Y-7 peptide is residues 131-142 of SEQ ID NO: 1; the Y-8 peptide is residues 131-142 of SEQ ID NO: 1. Residues 135-146; Y-9 peptide is residues 131-143 of SEQ ID NO: 1; Y-10 peptide is residues 135-147 of SEQ ID NO: 1; Y-11 peptide is SEQ ID NO: 1 The Y-12 peptide is residues 135-148 of SEQ ID NO: 1; the Y-13 peptide is residues 131-145 of SEQ ID NO: 1; the Y-14 peptide is SEQ ID NO: 1 Residues 135-149 of 1; Y-15 peptide is residues 131-146 of SEQ ID NO: 1; Y-16 peptide is residues 131-147 of SEQ ID NO: 1; Y-17 peptide is sequence. Residues 131-148 of No. 1; Y-18 peptide is residues 131-149 of SEQ ID NO: 1; Y-19 peptide is a scrambled / random sequence. It is a scatter plot matrix of all the results obtained with the peptide of set 1. It is the result of two-dimensional electrophoresis and Western blotting showing that the MIL38 antibody and the anti-GPC-1 antibody show overlapping reactivity in two-dimensional gel western blotting. FIG. 5 shows a Western blot of immunoprecipitation performed with MIL38 antibody or anti-GPC-1 antibody on a cell membrane protein extract of DU-145 prostate cancer or C3 (MIL38 negative). FIG. 5 shows a Western blot of immunoprecipitation showing that MIL38 antibody can detect glypican-1 in plasma (FIG. 16A) and prostate cancer extract (FIG. 16B) of prostate cancer patients. Each lane in FIG. 16A is 046IP NT-IP of prostate cancer plasma; 046IP HepI-IP of prostate cancer plasma treated with heparinase; 042IP NT-IP of normal control plasma; 042IP HepI-normal control plasma treated with heparinase. IP; Magic Mark-A commercially available protein marker that is a molecular weight standard.

Definitions The singular forms "a", "an" and "the" as used herein include a plurality of referents unless they have distinctly different meanings in the context. For example, "an antibody" also includes a plurality of antibodies.

As used herein, "comprising" means "inclusion." Variants of the word "comprising", such as "comprise" and "comprises", have various corresponding meanings. Thus, for example, a sample that "comprising" antibody A may consist solely of antibody A or may contain one or more additional components (eg, antibody B).

The term "plural" and "plurality" as used herein means more than one. In certain embodiments or embodiments, the plurality are 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, It can mean 46, 47, 48, 49, 50, 51 or more, as well as any integer that can be derived there and any range that can be derived there.

As used herein, the term "epitope" refers to a particular portion of an antigen that interacts with (eg, binds to) one or more binding entities, such as proteins, ligands, antibodies, antibody fragments or antibody derivatives. Refers to (s).

As used herein, the term "antibody (s)" refers to IgG (including IgG1, IgG2, IgG3 and IgG4), IgA (including IgA1 and IgA2), IgD, IgE, IgM and IgY, Includes all antibodies, including single-stranded whole antibodies, and their antigen-binding fragments. The antigen-binding antibody fragment is not particularly limited, but is limited to Fv, Fab, Fab'and F (ab') 2, Fd, single-chain Fvs (scFv), single-chain antibody, disulfide-bonded Fv (sdFv) and VL. Fragments containing either a domain or a VH domain can be mentioned. Antibodies can be of any animal origin or of appropriate production host. Antigen-binding antibody fragments, including single-chain antibodies, may contain the variable region (s) alone or with all or part of the hinge region, CH1 domain, CH2 domain and CH3 domain. In addition, any combination of the variable region (s) with the hinge region, CH1 domain, CH2 domain and CH3 domain is included. Antibodies can be monoclonal antibodies, polyclonal antibodies, chimeric antibodies, multispecific antibodies, humanized antibodies and human monoclonal antibodies and human polyclonal antibodies that specifically bind to a biomolecule. Antibodies can be bispecific antibodies, avibody, diabodies, tribodies, tetrabodies, nanobodies, single domain antibodies, VHH domains, human antibodies, fully humanized antibodies, partially humanized antibodies, anticarin, adonectin or affibody. ..

As used herein, the term "monoclonal antibody" is an antibody that recognizes a single antigenic epitope and is a naturally occurring variant that specifically binds to the same antigenic epitope and may be present in small amounts. Or refers to an antibody obtained from a substantially homogeneous population of antibodies that are identical except for (s).

As used herein, the term "humanized antibody" refers to various forms of antibody, including sequences derived from human and non-human antibodies (eg, mouse antibodies). For example, a humanized antibody has at least one in which all or substantially all hypervariable loops correspond to those of a non-human immunoglobulin and all or substantially all FR regions are derived from a human immunoglobulin sequence. One, usually two variable domains can be included substantially all. Optionally, the humanized antibody may also include at least a portion of an immunoglobulin constant region (Fc), which can usually be that of a human immunoglobulin.

As used herein, the term "chimeric antibody" refers to an antibody that exhibits the desired biological activity, wherein a portion of the light and / or heavy chain is derived from a given species or a particular species. Refers to an antibody that is identical or homologous to the corresponding sequence and whose remaining strand (s) is identical or homologous to the corresponding sequence of an antibody from another species. For example, a chimeric antibody may include a variable region derived from the first species and a constant region derived from the second species. Chimeric antibodies can be constructed, for example, by genetic engineering from immunoglobulin gene segments belonging to different species.

As used herein, the term "hybridoma" is created by fusion of immortal cells (eg, multiple myeloma cells) with antibody-producing cells (eg, B lymphocytes) to provide a single binding specificity. Refers to a cell capable of producing a possessing monoclonal antibody.

As used herein with respect to antibodies, antibody variants, antibody derivatives, antigen-binding fragments, etc., the term "specifically binds" refers to a given target molecule in preference to other non-target molecules. It means that it is possible to combine. For example, if an antibody, antibody variant, antibody derivative or antigen binding fragment (“molecule A”) is capable of specifically binding to a given target molecule (“molecule B”), then molecule A is a molecule. It has the ability to distinguish B from several other potential binding partners. Thus, when exposed to a variety of molecules that have equal potential for contact with molecule A as potential binding partners, molecule A selectively binds to molecule B, while other potential binding partners are substantially molecular A. And remain unbound. In general, molecule A preferentially binds molecule B at least 10-fold, preferably 50-fold, more preferably 100-fold, and most preferably greater than 100-fold as often as other potential binding partners. Molecule A may be able to bind to molecules other than Molecule B at a weak but detectable level. This is commonly known as a background bond and can be easily distinguished from a molecule B-specific bond, for example, by using an appropriate control.

The term "subject" as used herein includes any animal of economic, social or research importance, including cattle, horses, sheep, primates, birds and rodents. Thus, the "subject" can be a mammal, such as a human or non-human mammal.

As used herein with respect to a biomolecule (eg, an antibody), the term "isolated" refers to a biomolecule that does not contain at least some of the components associated with it in its native state.

As used herein, the terms "protein," "peptide," and "polypeptide," respectively, refer to polymers consisting of amino acids linked by peptide bonds and are used interchangeably. For the purposes of the present invention, a "polypeptide" may constitute a full-length protein or a portion of a full-length protein, meaning "peptide" and "polypeptide". There is no intentional difference.

As used herein, "conservative" amino acid substitution refers to replacing a given amino acid residue in an amino acid sequence with another different amino acid residue of approximately the same size and / or chemical properties. .. Non-limiting examples of conservative amino acid substitutions include A (Ala) to S (Ser) substitutions; R (arg) to K (lys) substitutions; N (asn) to Q (gl).
Substitution to n) or H (his); Substitution from D (asp) to E (glu); Substitution from Q (gln) to N (asn); Substitution from C (cys) to S (ser); Substitution from E (glu) to D (asp); substitution from G (gly) to P (pro).

As used herein, the term "polynucleotide" refers to single- or double-stranded polymers of deoxyribonucleotide bases, ribonucleotide bases, known analogs or natural nucleotides or mixtures thereof.

As used herein, the term "binding entity" includes any molecule capable of specifically binding to the GPC-1 epitope or mimetic thereof described herein. Non-limiting examples of binding entities include, for example, polypeptides such as antibodies.

As used herein, the term "kit" refers to any delivery system for delivering material. Such delivery systems include reaction reagents (eg, labels in appropriate containers, reference samples, auxiliary substances, etc.) and / or auxiliary materials (eg, buffers, instruction manuals for performing assays, etc.). Examples include systems that allow storage and transportation or delivery from one location to another. For example, the kit may include one or more containers such as boxes containing the relevant reaction reagents and / or auxiliary materials.

The term "positive control element" used herein in connection with a detection method or assay, when used in that method or assay, directly or indirectly generates a positive / positive signal, thereby producing a positive / positive signal. , Refers to an element that can at least partially or completely confirm that the method or assay can function properly.

When using the term "between" with respect to numbers in a range herein, it will be understood that the numbers at both ends of the range are included. For example, a polypeptide between 10 and 20 residues in length includes a 10-residue-long polypeptide and a 20-residue-long polypeptide.

It is acknowledged that the material or description derived from it is part of the general knowledge of the relevant technical field, even though this specification contains material or statements derived from that material. It's not a thing. Any material referred to herein is incorporated herein by reference in its entirety for the purpose of explanation, unless otherwise specified.

(Detailed explanation)
We have identified specific epitopes within glypican-1 (GPC-1) that are beneficial for detecting and quantifying GPC-1 levels using binding entities such as antibodies. Although these epitopes and combinations thereof are useful for many purposes, they can be targets for quantifying GPC-1 levels in prostate cancer diagnostic assays.

Accordingly, the present invention relates to GPC-1 epitopes and their components; combinations of said epitopes and / or epitope components; binding entities capable of specifically targeting epitopes, components and / or combinations; epitopes. Compositions, kits and other entities comprising components and / or combinations; methods of making binding entities capable of specifically targeting epitopes, components and / or combinations; and epitopes, components and / Or a method for diagnosing prostate cancer that requires detection of a combination.

Glypican-1 (GPC-1)
The present invention results from a series of epitopes within the glypican-1 heparan sulfate proteoglycan (GPC-1) that is the target of a specific binding entity (eg, an antibody).

Epitopes can be present in mammals such as GPC-1 proteins such as cows, horses, sheep, primates or rodents. Thus, the epitope can be present in a mammalian, eg, a GPC-1 protein such as a human or non-human mammal (eg, a canine GPC-1 protein).

In addition to or in lieu of the above, the epitope can be present in a non-mammalian GPC-1 protein, such as an avian GPC-1 protein.

The epitopes are human GPC-1 proteins (eg, NCBI reference sequence accession number NP_002072.2, GenBank accession number AAH51279.1, GenBank accession number AAA98132.1, GenBank accession number EAW71184.1, UniProtKB / Swiss-Prot It may be present in (defined by the sequence set forth in any one of accession numbers P35052.2 and / or SEQ ID NO: 14).

It will be appreciated that the epitope may also be present in a GPC-1 variant (eg, an isoform, splicing variant or allotype of GPC-1). Epitopes can be present in cell surface-bound and / or secretory GPC-1.

Epitope -Glypican-1 Epitope The present invention provides the GPC-1 epitope and its components, and also includes a combination of the epitope and / or the epitope component.

In some embodiments, the GPC-1 epitope according to the invention may include or consist of any one or more of the epitopes listed in Table 1 below.

In certain embodiments, the epitopes of the invention comprise or consist of multiple segments. These epitopes may be linear or discontinuous. Non-limiting examples of epitopes containing multiple segments are shown in Table 2 below.

In other embodiments, the present invention provides a combination of different epitopes comprising or consisting of a plurality of distinct epitopes. These distinct epitopes may be linear or discontinuous. A non-limiting example of an epitope combination containing a plurality of different epitopes is shown in Table 3 below.

The combination of epitopes according to the invention may include prostate-specific antigen (PSA), also known as gamma-seminoprotein or kallikrein-3 (KLK3). Therefore, the combination of epitopes according to the present invention includes any one of the epitopes listed in Table 1 or 2 in combination with PSA, or any one of the combinations of epitopes listed in Table 3. Can be further included in combination with PSA.

-Mutants The present invention provides variants of the GPC-1 epitope described herein.

Variants may include conservative or non-conservative amino acid substitutions (s) known to those of skill in the art.

In some embodiments, variants of the epitopes of the invention are identical in a particular percentage of amino acid residues (percentage of "sequence identity") over a particular region or, if not specified, throughout the sequence. .. Thus, the "mutants" of the GPC-1 epitope disclosed herein are at least 40%, 45%, 50%, 55%, 60%, with the sequences of the GPC-1 epitope described herein. It can have 65%, 70%, 75%, 80%, 83%, 85%, 88%, 90%, 93%, 95%, 96%, 97%, 98% or 99% sequence identity.

A variant may retain the same biological activity, substantially the same or altered biological activity as compared to the GPC-1 epitope sequence from which the variant originated.

The variant is derived from a different family, genus or species and has the same or substantially the same biological function or activity as the GPC-1 epitope sequence from which the variant originated (eg, a homologous GPC-1 epitope (eg,). , Derived from other species of mammals).

Differences in sequence identity can result from amino acid substitutions (eg, conservative and / or non-conservative substitutions), insertions and / or deletions. Conservative amino acid substitution, as is well known to those skilled in the art, refers to the replacement or replacement of one amino acid in a polypeptide chain with another amino acid having similar properties. For example, substituting glutamic acid (Glu), which is a charged amino acid, with aspartic acid (Asp), which is also a charged amino acid, can be said to be a conservative amino acid substitution.

The percentage of sequence identity between the two sequences can be readily determined using methods known to those of skill in the art. For example, the percentage of sequence identity between two sequences can be determined by comparing two optimally aligned sequences across a comparison window. The portion of the sequence comparison window is, for example, when compared to a reference sequence that contains no deletions or additions to optimally align the two sequences (eg, the GPC-1 epitope sequence described herein). It can contain deletions or additions (ie, gaps). Next, the number of matching positions for the nucleobase or amino acid residue in both sequences is calculated, the number of matching positions is divided by the total number of positions in the comparison window, and 100 is added to the result. The percentage of sequence identity can be calculated by multiplying to obtain the percentage of sequence identity.

The level of sequence identity can be measured using sequence analysis software (eg, 53705, Madison, Wisconsin, University Avenue 1710, University of Wisconsin Biotechnology Center, Sequence Analysis Software Package of the Genetics Computer Group). The software matches similar sequences by assigning a degree of homology to modifications, including various substitutions and deletions. Other examples of computer software suitable for measuring the degree of sequence identity between two sequences are, but are not limited to, the Clustal of the PC / Gene program (available from Intelligentics, Inc., Mountainview, CA). In addition to the ALIGN program (version 2.0), GCG Wisconsin Genetics Software Package, version 10 (available from Accellys, Inc., San Diego, San Diego, CA, USA), GAP, BESTFIT, BLAST, FASTA and TFASTA Can be mentioned.

Suitable and non-limiting examples of the mutants referred to in relation to the above embodiments, including those listed in Tables 1-3 above, are shown in Table 4 below.

Thus, variants of K V NP QGP GPEEK (SEQ ID NO: 1) comprises the 2-position V (val), 5-position Q (gln), P (pro ) to G (gly) and 7-position 6-position obtain. This variant may further contain K (lys) at position 1, N (asn) at position 3, and / or P (pro) at position 4. In addition to or in lieu of the above, the variant may further comprise G (gly) at position 8, P (pro) at position 9, and / or E (glu) at position 10. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6, 7 or 8 substitution residues. The substituted amino acid residue (s) is any one or more of the 1st, 3rd, 4th, 8th, 9th, 10th, 11th and / or 12th positions of SEQ ID NO: 1. Can exist in the position of.

Alternatively, variants of KVNPQ G P G P E EK (SEQ ID NO: 1), G (gly) in the 6-position may include E (glu) to G (gly) and 10-position to the 8-position. This variant may further contain N (asn) at position 3, Q (gln) at position 5, and / or P (pro) at position 7. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6, 7, 8 or 9 substitution residues. .. The substituted amino acid residue (s) is any one of the 1st, 2nd, 3rd, 4th, 5th, 7th, 9th, 11th and / or 12th positions of SEQ ID NO: 1. It can be in one or more positions.

Alternatively, variants of KVNPQG PG P E EK (SEQ ID NO: 1), P (pro) to the 7-position may include E (glu) to G (gly) and 10-position to the 8-position. This variant may further contain Q (gln) at position 5, G (gli) at position 6 and / or E (glu) at position 11. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6, 7, 8 or 9 substitution residues. .. The substituted amino acid residue (s) is any one of the 1st, 2nd, 3rd, 4th, 5th, 6th, 9th, 11th and / or 12th positions of SEQ ID NO: 1. It can be in one or more positions.

Variants of V NP QGP GPEEK (SEQ ID NO: 2) may contain V (val) at position 1, Q (gln) at position 4, G (gly) at position 5, and P (pro) at position 6. This variant may further contain N (asn) at the 2-position and / or P (pro) at the 3-position. In addition to or in lieu of the above, the variant may further contain G (gly) at position 7, P (pro) at position 8 and / or E (glu) at position 9. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6 or 7 substitution residues. Substituted amino acid residues (s) are located at any one or more of positions 2, 3, 7, 8, 9, 10, and / or 11 of SEQ ID NO: 2. Can exist.

Alternatively, variants of VNPQ G P G P E EK (SEQ ID NO: 2), G (gly) in the 5-position may include E (glu) to G (gly) and 9 the 7-position. This variant may further contain N (asn) at the 2-position, Q (gln) at the 4-position and / or P (pro) at the 6-position. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6, 7 or 8 substitution residues. The substituted amino acid residue (s) is any one or more of the 1st, 2nd, 3rd, 4th, 6th, 8th, 10th and / or 11th positions of SEQ ID NO: 2. Can exist in the position of.

Alternatively, variants of VNPQG PG P E EK (SEQ ID NO: 2), P (pro) in 6-position may include E (glu) to G (gly) and 9 the 7-position. This variant may further contain Q (gln) at the 4-position, G (gly) at the 5-position and / or E (glu) at the 10-position. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6, 7 or 8 substitution residues. The substituted amino acid residue (s) is any one or more of the 1st, 2nd, 3rd, 4th, 5th, 8th, 10th and / or 11th positions of SEQ ID NO: 2. Can exist in the position of.

Variants of V NP QGP GPEE (SEQ ID NO: 3) may contain V (val) at position 1, Q (gln) at position 4, G (gly) at position 5, and P (pro) at position 6. This variant may further contain N (asn) at the 2-position and / or P (pro) at the 3-position. In addition to or in lieu of the above, the variant may further contain G (gly) at position 7, P (pro) at position 8 and / or E (glu) at position 9. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, or 6 substitution residues. The substituted amino acid residue (s) may be present at any one or more of positions 2, 3, 7, 8, 9, and / or 10 of SEQ ID NO: 3. ..

Alternatively, variants of VNPQ G P G P E E (SEQ ID NO: 3), G (gly) in the 5-position may include E (glu) to G (gly) and 9 the 7-position. This variant may further contain N (asn) at the 2-position, Q (gln) at the 4-position and / or P (pro) at the 6-position. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6 or 7 substitution residues. Substituted amino acid residues (s) are located at any one or more of positions 1, 2, 3, 4, 6, 8, 8 and / or 10 of SEQ ID NO: 3. Can exist.

Alternatively, variants of VNPQG PG P E E (SEQ ID NO: 3), P (pro) in 6-position may include E (glu) to G (gly) and 9 the 7-position. This variant may further contain Q (gln) at the 4-position, G (gly) at the 5-position and / or E (glu) at the 10-position. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6 or 7 substitution residues. Substituted amino acid residues (s) are located at any one or more of positions 1, 2, 3, 4, 5, 8, and / or 10 of SEQ ID NO: 3. Can exist.

Variants of NP QGP GPEE (SEQ ID NO: 4) may contain Q (grn) at position 3, G (gly) at position 4, and P (pro) at position 5. The variant may further contain N (asn) at position 1 and / or P (pro) at position 2. In addition to or in lieu of the above, the variant may further contain G (gly) at position 6, P (pro) at position 7, and / or E (glu) at position 8. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, or 6 substitution residues. The substituted amino acid residue (s) may be present at any one or more of positions 1, 2, 6, 7, 8 and / or 9 of SEQ ID NO: 4. ..

Alternatively, variants of NPQ G P G P E E (SEQ ID NO: 4), G (gly) in the 4-position may include E (glu) to G (gly) and 8-position 6-position. This variant may further contain N (asn) at position 1, Q (gln) at position 3, and / or P (pro) at position 5. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, or 6 substitution residues. The substituted amino acid residue (s) may be present at any one or more of positions 1, 2, 3, 5, 7, and / or 9 of SEQ ID NO: 4. ..

Alternatively, variants of NPQG PG P E E (SEQ ID NO: 4), P (pro) at the 5-position may include E (glu) to G (gly) and 8-position 6-position. This variant may further contain Q (gln) at position 3, G (gly) at position 4, and / or E (glu) at position 9. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, or 6 substitution residues. The substituted amino acid residue (s) may be present at any one or more of positions 1, 2, 3, 4, 7, and / or 9 of SEQ ID NO: 4. ..

Variants of K V NP QGP GPE (SEQ ID NO: 5), V (val) at the 2-position, Q (gln) at the 5-position may include P (pro) to G (gly) and 7-position 6-position. This variant may further contain K (lys) at position 1, N (asn) at position 3, and / or P (pro) at position 4. In addition to or in lieu of the above, the variant may further comprise G (gly) at position 8, P (pro) at position 9, and / or E (glu) at position 10. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, or 6 substitution residues. The substituted amino acid residue (s) may be present at any one or more of positions 1, 3, 4, 8, 9, and / or 10 of SEQ ID NO: 5. ..

Alternatively, variants of KVNPQ G P G P E (SEQ ID NO: 5), G (gly) in the 6-position may include E (glu) to G (gly) and 10-position to the 8-position. This variant may further contain N (asn) at position 3, Q (gln) at position 5, and / or P (pro) at position 7. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6 or 7 substitution residues. Substituted amino acid residues (s) are located at any one or more of positions 1, 2, 3, 4, 5, 7, 7 and / or 9 of SEQ ID NO: 5. Can exist.

Alternatively, variants of KVNPQG PG P E (SEQ ID NO: 5), P (pro) to the 7-position may include E (glu) to G (gly) and 10-position to the 8-position. This variant may further contain Q (gln) at position 5 and / or G (gly) at position 6. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6 or 7 substitution residues. Substituted amino acid residues (s) are located at any one or more of positions 1, 2, 3, 4, 5, 6, and / or 9 of SEQ ID NO: 5. Can exist.

Variants of K V NP QGP GP (SEQ ID NO: 6), the 2-position V (val), 5-position Q (gl
n), G (gly) at the 6th position and P (pro) at the 7th position may be included. This variant may further contain K (lys) at position 1, N (asn) at position 3, and / or P (pro) at position 4. In addition to or in lieu of the above, this variant may further comprise G (gly) at position 8 and / or P (pro) at position 9. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, or 5 substitution residues. The substituted amino acid residue (s) may be present at any one or more of positions 1, 3, 4, 8 and / or 9 of SEQ ID NO: 6.

Variants of KVNPQ G P G P (SEQ ID NO: 6) may include a G (gly) to G (gly) and 8-position 6-position. This variant may further contain N (asn) at position 3, Q (gln) at position 5, and / or P (pro) at position 7. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6 or 7 substitution residues. Substituted amino acid residues (s) are located at any one or more of positions 1, 2, 3, 4, 5, 7, 7 and / or 9 of SEQ ID NO: 6. Can exist.

A variant of KVNPQG PG P (SEQ ID NO: 6) may contain P (pro) at position 7 and G (gly) at position 8. This variant may further contain Q (gln) at position 5 and / or G (gly) at position 6. In addition to or in place of the above, this variant may contain 1, 2, 3, 4, 5, 5, 6 or 7 substitution residues. Substituted amino acid residues (s) are located at any one or more of positions 1, 2, 3, 4, 5, 6, and / or 9 of SEQ ID NO: 6. Can exist. Variants of any one of the epitopes of the invention represented by SEQ ID NOs: 7-13 may contain amino acid substitutions at any one or more positions of the epitope sequence. The amino acid substitution may be a conservative amino acid substitution known to those skilled in the art or a non-conservative amino acid substitution. Variants can be conservative substitutions (s) only, non-conservative substitutions (s) only or combinations of conservative substitutions (s) and non-conservative substitutions (s). Can include.

-Fragments The present invention provides fragments of the GPC-1 epitopes and variants described herein.

In some embodiments, the epitope fragments of the invention are 4, 5, 6, 7, 8, 9, 10, 11, 12, 12, 13, 14, 15, 15. , 16, 17, 18, 19 or 20 amino acids may be contained or consist of. Thus, the epitope fragments according to the invention are, for example, 5-10 amino acids, 5-15 amino acids, 5-20 amino acids, 10-20 amino acids, 10-15 amino acids, 7-15 amino acids, 7-13 amino acids, 8 in length. It may contain or consist of ~ 12 amino acids, 8-10 amino acids, 11-19 amino acids, 12-18 amino acids or 13-17 amino acids. Fragments of full-length GPC-1 epitopes disclosed herein may generally have immunological properties comparable to or, in some cases improved from, full-length GPC-1 epitopes.

Suitable and non-limiting examples of the fragments referred to in relation to the above embodiments, including those listed in Tables 1 to 4 above, are shown in Table 5.

-Fusion Polypeptide A particular embodiment of the invention provides a GPC-1 epitope in the form of a fusion polypeptide. For example, two or more full-length epitopes selected from Table 1, two or more epitope segments selected from Table 2, a combination of two or more full-length epitopes selected from Table 3, or the full length of Table 1. Combinations of epitopes with any one or more epitopes selected from Table 2 can be linked to form fusion polypeptides.

Fusion polypeptides can be prepared using standard techniques known to those of skill in the art, including, for example, chemical conjugation. In addition, the fusion polypeptide may be expressed as a recombinant polypeptide in the expression system. For example, the DNA sequences encoding the polypeptide components of the fusion polypeptide can be assembled separately and ligated into the appropriate expression vector. A DNA sequence encoding a second polypeptide component with or without a peptide linker at the 3'end of a DNA sequence encoding a polypeptide component so that the leading frame of the sequence is in-frame. Can be ligated to the 5'end of. This allows translation into a single fusion polypeptide that retains the biological activity of both polypeptide components.

Linker sequences are used to ensure that the first and second polypeptide components of the fusion protein are folded into the appropriate secondary and / or tertiary structure of each polypeptide component. Can be separated with sufficient distance. Non-limiting examples of suitable linkers include convenient spacer molecules such as peptides / polypeptides, alkyl chains known to those of skill in the art. It is capable of a flexible elongated configuration and has a secondary structure that can interact with the functional epitope (s) within the polypeptide component (s) of the fusion polypeptide. It is impossible and / or hydrophobic and / or charged residues capable of reacting with the functional epitope (s) within the polypeptide component (s) of the fusion polypeptide. Appropriate peptide linker sequences can be selected depending on factors, including the absence of.

To give just a non-limiting example, the peptide linker sequence may contain Gly, Asn and / or Ser residues. In addition to, or in lieu of, other near-neutral amino acids such as Thr and Ala may be used in the peptide linker sequence. Further examples of amino acid sequences that may be usefully used as linkers include US Pat. No. 4,935,233; US Pat. No. 4,751,180; Murphy et al., Proc. Natl. Acad. Sci. USA 83: 8258-8262, 1986; and Maratea et al., Gene 40: 39-46, 1985. The linker sequence can generally be 1 to about 50 amino acids in length. Therefore, the linker sequence has a length of 5 amino acids, 10 amino acids, 15 amino acids, 20 amino acids, 30 amino acids, 40 amino acids, 10-50 amino acids, 10-40 amino acids, 10-30 amino acids, 20-30 amino acids, 1-5. It can be an amino acid or 5-10 amino acids. The fusion polypeptide according to the invention is a non-essential N-terminal amino acid region in which the first and second polypeptide components of the fusion polypeptide can be used to separate functional domains and prevent steric damage. If you have, you may not need a linker sequence.

-Polynucleotides, vectors and host cells The present invention also comprises fusion proteins comprising the GPC-1 epitopes (s) of the invention, segments of GPC-1 epitopes and GPC-1 epitopes and / or segments thereof. Provided is a polynucleotide to be encoded.

This polynucleotide can be cloned into a vector. The vector may include, for example, a DNA, RNA or complementary DNA (cDNA) sequence encoding a GPC-1 epitope, a GPC-1 epitope segment (s) and / or a fusion protein. The vector can be a plasmid vector, a viral vector or any other suitable medium adapted for insertion of a foreign sequence, intracellular introduction of the foreign sequence and expression of the introduced sequence. Usually, the vector is an expression vector and may include expression control and processing sequences such as promoters, enhancers, ribosome binding sites, polyadenylation signals and transcription termination sequences.

The present invention also contemplates host cells transformed with the above vectors. For example, the polynucleotide of the invention can be cloned into a vector and transformed into a bacterial host cell, such as E. coli.

Methods of vector construction and transformation of the vector into the host cell are generally known in the art, such as Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory Press, Plainview, New York. Ausube F. M. Et al. (E.), Current Protocols in Molecular Biology (2007), John Wiley and Sons, Inc. It is described in.

-Preparation A fusion protein containing the GPC-1 epitope, a segment of the GPC-1 epitope and the GPC-1 epitope and / or the segment thereof of the present invention can be produced according to a standard methodology well known to those skilled in the art.

Epitopes, segments and fusion proteins can also be prepared using any of a variety of well-known synthetic and / or recombinant techniques. Polypeptides can be made, for example, by synthetic means using methodologies well known to those of skill in the art. In one non-limiting example, a commercially available solid phase technique (eg, Merrifield's solid phase synthesis method) in which amino acids are sequentially added to extend the amino acid chain can be used (Merlifeeld, J. Am. Chem. Soc. 85). : 2149-2146, 1963). Devices for automatically synthesizing epitopes, segments and fusion proteins disclosed herein are commercially available (eg, PerkinElmer / Applied Biosystems Division (Foster City, CA), according to the manufacturer's instructions. Can be used.

In addition to or in place of the above, epitopes, segments and fusion proteins may be made by any other method available to those of skill in the art. For example, recombinant means may be used, in which the nucleic acid encoding the selected epitope (s), segment (s) and / or fusion protein (s) may be used. It can be inserted into an expression vector using any of a variety of methods known in the art (eg, Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory Press, Cold Spring). N. Y.; Sambrook and Russell, Molecular Cloning: A Laboratory Manual, third Edition (Jan.15,2001) Cold Spring Harbor Laboratory Press, ISBN: 0879695765; Ausubel et al, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, NY (1989)). Standards known to those of skill in the art for the construction of suitable expression vectors containing nucleic acids encoding selected epitopes (s), segments (s) and / or fusion proteins (s). Use ligation technology.

The ligated nucleic acid sequence can be actuated with a suitable transcriptional or translational regulatory element that promotes expression of the epitope (s), segment (s) and / or fusion protein (s). Can be linked. Regulatory elements involved in protein expression can be located on the 5'side of the coding region of the polypeptide. Stop codons and transcription termination signals that terminate translation are present on the 3'side of the nucleic acid sequence encoding the epitope (s), segment (s) and / or fusion protein (s). obtain. After constructing a nucleic acid encoding the polypeptide of interest (s) with operably linked regulatory elements, the resulting expression cassette is introduced into the host cell and the encoded polypeptide (1). One or more) can be expressed.

In the present invention, the GPC-1 epitope, the segment of the GPC-1 epitope and the fusion protein containing the GPC-1 epitope and / or the segment thereof can be "isolated". An "isolated" polypeptide is a polypeptide that has been removed from its original environment. For example, a native protein or polypeptide referred to herein is considered isolated if it is separated from some or all of the substances that coexist in the natural system. The isolated polypeptides referred to herein may be purified. For example, an isolated polypeptide can be at least about 90% pure, at least about 95% or at least about 99% pure.

The polynucleotides and nucleic acids according to the invention are generally known in the art and are described, for example, by Ausubel F. et al. M. Et al. (Ed.), Current Protocols in Molecular Biology (2007), John Sambrook and Sons, Inc; Sambrook et al. (1989) Molecular Cloning: A Laboratory Biology Male, Color (2nd edition), Molecular Cloning: A Laboratory, Et al., Molecular Cloning (1982), 280-281. Polynucleotides are described, for example, in chemical synthesis techniques, such as phosphodiester and phosphotriester methods (eg, Narg SA et al. (1979) Meth. Enzymol. 68: 90; see Brown, EL (1979) et al., Meth. Enzymol. 68: 109; and US Pat. No. 4,356,270), diethyl phosphoramidite method (Beaucage SL et al. (1981) Tetrahedron (See Letters, 22: 1859-1862). A method of synthesizing an oligonucleotide on a modified solid support is described in US Pat. No. 4,458,066.

-Support The epitope and fusion polypeptide according to the invention may be attached to the support. The support can be, for example, an insoluble material or substrate that retains the epitope and does not move it freely in most of the reaction mixture. Suitable supports for immobilizing or localizing epitopes and fusion polypeptides are well known to those of skill in the art. The support is a wide variety of substrates in various forms, including beads that are convenient for use in microassays, plastic and glass plates with separate wells, and other materials that are compatible with the reaction conditions. , Polymer, etc. can be selected. In certain preferred embodiments, the support can be a plastic material, a plastic bead or wafer, or a plastic well or tube for performing a particular assay (eg, ELISA).

Binding Entity The present invention provides a binding entity capable of specifically binding to the GPC-1 epitope described herein.

The binding entity can be any molecule capable of specifically binding to the GPC-1 epitope described herein. Non-limiting examples of binding entities include polypeptides, antibodies, antibody fragments, molecular imprints, lectins and capture compounds. The binding entity can bind to the GPC-1 epitope of the invention or another different region of GPC-1, as well as between the epitope and another different binding entity, such as an antibody disclosed herein. It can also be an agent that can also modify binding interactions.

Binding entities such as antibodies capable of specifically binding to the GPC-1 epitope of the invention preferentially bind to a given target epitope, combination of epitope segments or combination of epitopes over other non-target molecules. can do. For example, if the binding entity (“Molecule A”) is capable of specifically binding to a given target GPC-1 epitope (“Molecule B”), then the molecule A is the molecule B and some others. Has the ability to distinguish from another potential binding partner of. Thus, when exposed to a variety of molecules that have equal potential for contact with molecule A as potential binding partners, molecule A selectively binds to molecule B, while other potential binding partners are substantially molecular A. And remain unbound. In general, molecule A preferentially binds molecule B at least 10-fold, preferably 50-fold, more preferably 100-fold, and most preferably greater than 100-fold as often as other potential binding partners. Molecule A may be able to bind to molecules other than Molecule B at a weak but detectable level. This is commonly known as a background bond and can be easily distinguished from a molecule B-specific bond, for example, by using an appropriate control.

Once the specific GPC-1 epitope provided herein is known, one of ordinary skill in the art can make a binding entity without effort for the invention. For example, known techniques can be used to prepare polyclonal and monoclonal antibody preparations that specifically bind to the GPC-1 epitopes (s) of the invention.

Any technique can be used to produce a monoclonal antibody against the target GPC-1 epitope in a cultured continuous cell line. For general methodologies, see Harlow and Lane (eds.), (1988), "Antibodies-A Laboratory Manual", Cold Spring Harbor Laboratory, N. et al. Y. It is described in. As a specific methodology, the hybridoma technology first developed by Kohler (1975) (“Continuous cells of fused cells secreting antibody of predefined specificity”, Nature, 256: 495-4), Nature, 256: 495-4 Techniques (Kozbor et al., (1983), "The Production of Monoclonal Antibodies From Human Lymphocytes", Immunology Today, 4: 72-79) and EB Hybridoma (Technology) to produce human monoclonal antibodies, EB Hybridoma and
Cancer Therapy ”, pp. 77-96, Alan R. Liss, Inc. ). Immortal antibody-producing cell lines can be made by techniques other than fusion, such as direct transformation of B lymphocytes with carcinogenic DNA or transfection with Epstein-Barr virus (eg, M. Schreier et al., (1980). ), "Hybridoma Techniques", Cold Spring Harbor Laboratory; Hammerling et al., (1981), "Monoclonal Antibodies and T-cell Hybridomas", Elsevier / North-Holland Biochemical Press, Amsterdam; Kennett et al., (1980), "Monoclonal Antibodies", See Plenum Press).

Briefly, the means for producing hybridomas that produce monoclonal antibodies are hyperpermanent in self-perpetuating cell lines such as myeloma and their cognitive factor binding moieties, cognitive factors or their replication origin-specific DNA binding moieties. It can be fused with lymphocytes collected from the spleen of an immunized mammal. Hybridomas that produce monoclonal antibodies capable of specifically binding to the GPC-1 epitopes of the invention are identified by their ability to respond immune to the presented epitope (s).

Monoclonal antibodies useful in the practice of the present invention can be made by initiating culturing of monoclonal hybridomas comprising a nutrient medium containing hybridomas that secrete antibody molecules of appropriate antigen specificity. The culture is maintained under conditions sufficient for the hybridoma to secrete antibody molecules into the medium for a period sufficient for such secretion. The antibody-containing medium is then collected. The antibody molecule can then be further isolated by well-known techniques.

Similarly, there are various methods known in the art that can be used to make polyclonal antibodies. The production of polyclonal antibodies against a given GPC-1 epitope combination sensitizes a variety of host animals, including but not limited to rabbits, chickens, mice, rats, sheep, goats, etc., by injection of the epitope. be able to. In addition, the target molecule can be conjugated to an immunogenic carrier (eg, bovine serum albumin (BSA) or keyhole limpet hemocyanin (KLH)). In addition, without particular limitation, Freund (complete and incomplete) adjuvants, inorganic gels such as aluminum hydroxide, surfactants such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins. The immune response can be enhanced with a variety of adjuvants, including dinitrophenol and adjuvants believed to be useful for humans such as BCG (Calmet gellan bacillus) and Corynebacterium parvum.

Screening for the desired antibody can be performed by a variety of techniques known in the art. The assay suitable for examining the immunospecific binding of an antibody is not particularly limited, but is limited to radioimmunoassay, ELISA (enzyme-binding immunoassay), sandwich immunoassay, immunoradiommunoassay, gel diffusion precipitation reaction, and immunodiffusion assay. , In situ immunoassay, western blot, sedimentation reaction, aggregation assay, complement binding assay, immunofluorescence assay, protein A assay, immunoelectrommunoassay assay, etc. (eg, Ausube et al., (1994), "Current Protocols in".
Molecular Biology ”, Volume 1, John Wiley & Sons, Inc. , New York). Antibody binding can be detected by a detectable label on the primary antibody. Alternatively, the antibody may be detected by binding to an appropriately labeled secondary antibody or reagent. Various methods of detecting binding in an immunoassay are known in the art and are within the scope of the present invention.

Antibodies (or fragments thereof) to a specific GPC-1 epitope (s) of interest exhibit binding affinity to that epitope (s). Preferably, the antibody (or fragment thereof) binding affinity or avidity of about ¹⁰ 5 ^{M -1,} more preferably above about ¹⁰ 6 ^{M -1} greater, even more preferably about ¹⁰ 7 ^{M -1} greater than, and most preferably is about ¹⁰ 8 ^{M -1} greater.

From the perspective of obtaining the appropriate amount of antibody according to the invention, batch fermentation with serum-free medium can be used to produce the antibody (s). After fermentation, the antibody can be purified by a multi-step method incorporating the steps of chromatography and virus inactivation / removal. For example, the antibody can be first separated by protein A affinity chromatography and then treated with a solvent / detergent to inactivate the lipid enveloped virus. Further purification, usually anion and cation exchange chromatography, can be used to remove the remaining proteins, solvents / detergents and nucleic acids. The purified antibody is further purified using a gel filtration column and formulated with 0.9% saline. The formulated bulk preparation can then be sterilized and virus filtered and subdivided.

Non-limiting examples of antibodies capable of binding to one or more GPC-1 epitopes of the invention include.
(I) MIL38 antibody deposited with Accession No. CBA20140026 to Cellbank Australia (Hawkesbury Road 214, Westmead, NSW2145, Australia) on August 22, 2014 in accordance with the provisions of the Budapest Treaty;
(Ii) Anti-glypican 1 / GPC1 antibody (ab137604): A rabbit polyclonal antibody (IgG) specific for human GPC-1, which is commercially available from abcam (registered trademark) (http://www.abcam. com / glycocan-1-gpc1-antibody-ab137604.html);
(Iii) MAB2600 | Anti-glypican-1 antibody, clone 4D1: A mouse monoclonal antibody (IgG _k ) specific for human and rat GPC-1, which is commercially available from Millipore (http://www.emdmillipore). .Com / AU / en / product /, MM_NF-MAB2600? Cid = BI-XX-BRC-A-BIOC-anti-B033-1308);
(Iv) Goat Anti-Glypican 1 Antibody (AA24-530): A goat polyclonal antibody specific for human GPC-1, which is commercially available from LifeSpan BioSciences (https://www.lsbio.com/antibodies / antibody). See gpc1-antibody-glypican-antibody-aa24-530-icc-wb-western-flow-ls-c330760 / 341104).

Compositions and Kits The compositions and kits according to the invention may include:
-One or more GPC-1 epitopes, variants or fragments thereof described herein (eg, Table 1);
-One or more GPC-1 epitope segments, variants or fragments thereof described herein (eg, Table 2);
-A combination of one or more GPC-1 epitopes described herein (eg, Table 3);
-One or more fusion proteins comprising the GPC-1 epitopes (s), segments (s) of GPC-1 epitopes (s) and / or variants or fragments thereof described herein. (See the subsection entitled "Fusion Polypeptides"); and / or-one or more binding entities described herein (see the subsection entitled "Binding Entities" above). ..

The composition may further comprise an acceptable carrier, auxiliary agent and / or diluent. Carriers, diluents and auxiliaries can be "acceptable" in terms of compatibility with other components of the composition and / or are generally harmless to any recipient thereof. It can be "pharmaceutically acceptable". Suitable carriers, diluents and auxiliaries are well known to those of skill in the art (eg, Gilman et al., eds., Goodman and Gilman's: the pharmacological bases of theapeutics, 8th edition, Pergamon Press (1990); Rem. See Pharmacological Sciences, Mack Publishing Co .: Easton, Pa., 17th Edition (1985)). In some embodiments, the composition may be used for diagnostic or research purposes.

The kit may be a subdivided kit or a grouped kit. "Subdivided kit" refers to a delivery system that includes two or more separate containers, each containing subparts of all the components of the kit. Any delivery system that includes two or more separate containers, each containing a subpart of the entire component of the kit, is within the meaning of the term subdivided kit. "Bulk kit" refers to a delivery system in which all components of the kit are contained in a single container (eg, a single box containing each desired component). In some embodiments, the kit may be used for diagnostic or research purposes.

Diagnostic Method The GPC-1 epitope of the present invention, the segment of the GPC-1 epitope and the fusion protein containing the GPC-1 epitope and / or the segment thereof can be used in the diagnostic method. Specifically, we have discovered that glypican-1 is a novel marker for prostate cancer (Walsh et al., "Cell Surface Prostate".
US Patent Provisional Application No. 61/928/776 (unpublished) entitled "Cancer Antigen for Diagnosis").

Therefore, the present invention is based on the detection of GPC-1 epitopes (s), GPC-1 epitope segments and / or variants and fragments of epitopes / epitope segments described herein, and the prostate of interest. Provided are methods for diagnosing cancer, predicting prognosis, or predicting the likelihood that a subject will develop prostate cancer. In addition to or in place of the above, variants and fragments of the GPC-1 epitope and / or GPC-1 epitope fragments can be detected diagnostically.

The above method generally involves determining the level of the GPC-1 epitope (s) and / or the GPC-1 epitope segment in a biological sample from the subject. In performing this method, in addition to or in place of the above, the level of mutants (s) and fragments of the GPC-1 epitope and / or its segments may be determined. Non-limiting examples of GPC-1 epitopes, GPC-1 epitope segments and variants and fragments are those referred to in the section entitled "Epitopes" (in particular, Tables 1-3 and related variants and fragments. Please refer to the explanation of).

This method determines the level of prostate-specific antigen (PSA), also known as gamma-seminoprotein or kallikrein-3 (KLK3), in biological samples, as well as optionally controls the level of detected PSA. It may further include comparing with that of.

In some embodiments, the level of the GPC-1 epitope (s), the GPC-1 epitope segment and / or the variant and fragment of the epitope / epitope segment detected in the biological sample of interest, and the control sample. It can be compared with the levels found to be present in. The level in the control sample can be determined before, when, or after determining the level present in the biological sample of interest. To give a non-limiting example, the level present in a control sample can be determined based on the level present in an equivalent biological sample derived from an individual or the average level present in a biological sample derived from a population. The individual (s) can be an individual already known not to have cancer and / or an individual already known not to have prostate cancer. In general, detection of higher levels in a subject's biological sample than in a control is considered to indicate that the subject has or is more likely to develop prostate cancer. For example, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, or at least 60% higher is an indicator that a subject has or is more likely to develop prostate cancer. obtain. Alternatively, if the level in the subject's biological sample is detected to be equal to or lower than that of the control, the subject does not have or is not likely to develop prostate cancer. It is thought to indicate that.

In some embodiments, the GPC-1 epitopes (s), GPC-1 epitope segments and / or variants and fragments of the epitope / epitope segments described herein are positive for the diagnostic methods of the invention. Used as a control. For example, they can be used in a given assay to detect GPC-1 epitopes (s), GPC-1 epitope segments and / or variants and fragments in that assay performed. To confirm.

In some embodiments, the fusion proteins of the invention (s) are used in the diagnostic methods of the invention. The subsection entitled "Fusion Proteins" contains non-limiting examples of suitable fusion proteins. The fusion protein (s) can be used as a positive control in the detection method.

The biological sample can be a tissue sample (eg, a biopsy sample of prostate tissue) or a body fluid sample.

The body fluid sample can be a blood, serum, plasma or urine sample.

Non-limiting examples of prostate cancer that can be detected in the present invention include intraprostatic neoplasia, adenocarcinoma, leiomyosarcoma and rhabdomyosarcoma.

Detection of GPC-1 epitopes, GPC-1 epitope segments and variants and fragments is not particularly limited, but is not limited to a particular detection method, but is not particularly limited, but Western blot analysis. , Enzyme-linked immunosorbent assay (ELISA), fluorescent labeling cell sorting (FACS), biofilm testing or affinity ring test (see, eg, US Patent Application Publication No. 2013/016,736). It can be by standard assays known to those of skill in the art. Binding entities according to the invention can be used in these assays.

In some embodiments, the binding entity is an antibody. In other embodiments, the waiting entity is not an antibody.

In some embodiments, the antibody is selected from one or more of the following:
(I) MIL38 antibody deposited with Accession No. CBA20140026 to Cellbank Australia (Hawkesbury Road 214, Westmead, NSW 2145, Australia) on August 22, 2014 in accordance with the provisions of the Budapest Treaty;
(Ii) Anti-glypican 1 / GPC1 antibody (ab137604): A rabbit polyclonal antibody (IgG) specific for human GPC-1, which is commercially available from abcam (registered trademark) (http://www.abcam. com / glycocan-1-gpc1-antibody-ab137604.html);
(Iii) MAB2600 anti-glypican-1 antibody, clone 4D1: A mouse monoclonal antibody (IgG _k ) specific for human and rat GPC-1, which is commercially available from Millipore (http://www.emdmillipore. com / AU / en / product /, MM_NF-MAB2600? Cid = BI-XX-BRC-A-BIOC-anti-B033-1308);
(Iv) Goat Anti-Glypican 1 Antibody (AA24-530): A goat polyclonal antibody specific for human GPC-1, which is commercially available from LifeSpan BioSciences (https://www.lsbio.com/antibodies / antibody). See gpc1-antibody-glypican-antibody-aa24-530-icc-wb-western-flow-ls-c330760 / 341104).

In some embodiments, the antibody is not selected from one or more of the following:
(I) MIL38 antibody deposited with Accession No. CBA20140026 to Cellbank Australia (Hawkesbury Road 214, Westmead, NSW2145, Australia) on August 22, 2014 in accordance with the provisions of the Budapest Treaty;
(Ii) Anti-glypican 1 / GPC1 antibody (ab137604): A rabbit polyclonal antibody (IgG) specific for human GPC-1, which is commercially available from abcam (registered trademark) (http://www.abcam. com / glycocan-1-gpc1-antibody-ab137604.html);
(Iii) MAB2600 anti-glypican-1 antibody, clone 4D1: A mouse monoclonal antibody (IgG _k ) specific for human and rat GPC-1, which is commercially available from Millipore (http://www.emdmillipore. com / AU / en / product /, MM_NF-MAB2600? Cid = BI-XX-BRC-A-BIOC-anti-B033-1308);
(Iv) Goat Anti-Glypican 1 Antibody (AA24-530): A goat polyclonal antibody specific for human GPC-1, which is commercially available from LifeSpan BioSciences (https://www.lsbio.com/antibodies / antibody). See gpc1-antibody-glypican-antibody-aa24-530-icc-wb-western-flow-ls-c330760 / 341104).

In some embodiments, the binding entity comprises the MIL38 antibody (CBA20140026), TQNARA (SEQ ID NO: 8), ALSTASDDR (SEQ ID NO: 9), PSERPP (SEQ ID NO: 10), QDASDDGSGS (SEQ ID NO: 11), LGPECSRAVMK (SEQ ID NO: 11). Anti-glypican 1 (GPC-1) antibody-free antibody capable of binding to an epitope containing an amino acid sequence selected from any one or more of No. 13) and TQNARAFRD (SEQ ID NO: 7). It is a group.

Those skilled in the art will appreciate that a number of modifications and / or modifications can be made to the invention disclosed in the form of specific embodiments without departing from the broadly described gist and scope of the invention. .. Therefore, embodiments of the present invention should be considered to be exemplary in all respects and not limiting.

From this, the present invention will be described with reference to specific examples, but these should by no means be construed as limiting.

Example 1: Identification and characterization of a glypican-1 epitope to which mouse anti-human glypican 1 (MIL38-AM4) binds 1.1. Materials and Methods Experimental sets covering reference sequences with various conformational constraints were made and antibodies were probed with peptide arrays.

-Antibodies The mouse anti-human gripican 1 monoclonal antibody MIL38-AM4 was prepared as shown in Table 6 below.

-Peptide Structured The following human gripican-1 (GPC-1) sequence was used as the basis for preparing a library of peptides.

A rendered image of the chain B existing as Protein Data Bank identification number (PBD ID) 4AD7 (http://www.ebi.ac.uk/pdbsum/4AD7) is shown in FIG. 1A.

-Chemically Linked Peptides on Scaffolds (CLIPS) Technology The general principles of CLIPS technology used are described below.

CLIPS technology immobilizes the structure of a peptide into a defined three-dimensional structure. This allows even the most complex binding site function to be mimicked. CLIPS technology is now routinely used to make peptide libraries into single, double or triple loop structures as well as sheet-like and helix-like folds.

A CLIPS reaction occurs between the bromo group of the CLIPS scaffold and the thiol side chain of cysteine. This reaction is fast and specific under mild conditions. This chemical reaction was used to transform the intrinsically disordered protein sequence into a variety of structures, including single T2 loops, T3 double loops, T2 and T3 loop conjugates, stabilized beta sheets and stabilized alpha helices. Convert to a CLIPS construct having (Timerman et al., J. Mol. Chemist. 2007; 20: 283-29).

CLIPS library screening begins with the conversion of the target protein into a library of up to 10,000 overlapping peptide constructs using a combinatorial substrate design. A substrate for the linear peptide is synthesized on a solid support, which then takes the form of a spatially defined CLIPS construct. Constructs in which both parts of the discontinuous epitope are in the correct conformation bind to the antibody with high affinity and are detected and quantified. Constructs with incomplete epitopes bind to the antibody with lower affinity, whereas constructs without epitopes do not bind at all. Information on affinity is used for iterative screening to reveal the sequence and conformational details of the epitope.

Convert target proteins containing discontinuous conformational epitopes into a substrate library. Combinatorial peptides are synthesized on the patented minicard and chemically converted into spatially defined CLIPS constructs. Quantify antibody binding.

-Peptide synthesis A library of structured peptides was synthesized to reconstruct the discontinuous epitopes of the target molecule. This synthesis was carried out using the Chemically Linked Peptides on Scaffolds (CLIPS) technique. CLIPS technology has allowed the production of structured peptides of single loops, double loops, triple loops, sheet-like folds, helix-like folds and combinations thereof. The CLIPS template was attached to a cysteine residue. The side chains of multiple cysteines within the peptide were combined with one or two CLIPS templates. For example, a 0.5 mM solution of T2 CLIPS template 1,3-bis (bromomethyl) benzene was dissolved in ammonium hydrogen carbonate (20 mM, pH 7.9) / acetonitrile (1: 1 (v / v)). This solution was added onto a peptide array. The CLIPS template was attached to the side chains of two cysteines present in the solid phase binding peptide of the peptide array (well plate with 4553 μl wells). The peptide array was completely covered with solution and gently shaken in solution for 30-60 minutes. Finally, washed thoroughly peptide array with excess _{H 2} O, beta SDS / 0.1% of 1% in PBS (pH 7.2) - in disruption buffer containing mercaptoethanol, at 70 ° C. 30 after sonication minutes and sonicated for another 45 minutes in H 2 _O. T3 CLIPS carrying the peptide was prepared by the same method except that there were three cysteines.

Linear peptides and CLIPS peptides were chemically synthesized according to the following design:

-ELISA screening Binding of the antibody to each synthetic peptide was tested with a PEPSCAN-based ELISA. The peptide array was incubated with the primary antibody solution (4 ° C. overnight). After washing, the peptide array was incubated with a 1/1000 diluted antibody peroxidase conjugate (SBA, Catalog No. 2010-05) at 25 ° C. for 1 hour. After washing, the peroxidase substrate 2,2'-azino-di-3-ethylbenzothiazolin sulfonate (ABTS) and 2 μl / ml of 3% H ₂ O ₂ were added. After 1 hour, the color development was measured. Color development was quantified with a charge coupling element (CCD) camera and image processing system.

-Data processing Values obtained with a CCD camera ranged from 0 to 3000 mAU, much the same as a standard 96-well plate ELISA reader. This result was quantified and stored in the Peplab database. Occasionally, there were wells containing air bubbles and showing false positive values. The cards were manually examined and all bubble values scored 0.

-Synthetic quality control In order to confirm the quality of the synthetic peptide, a pair of positive control peptide and negative control peptide was synthesized separately in parallel. This was screened for antibody 57.9 (see Postumus et al., J. Virology, 1990, 64: 3304-3309).

-Details of screening Table 7 summarizes the antibody binding conditions. For Pepscan buffer and preparation (SQ), the numbers represent the relative amount of competing protein (combination of horse serum and ovalbumin).

1.2. Results-Main experimental results and determination of signal-to-noise ratio Figure 2 graphs an overview of the entire dataset of untreated ELISA results obtained by screening. In this figure, a boxplot shows each dataset and represents the mean ELISA signal, distribution and outliers within each dataset. Various ELISA data distributions were obtained according to the experimental conditions (antibody amount, blocking intensity, etc.). Epitopes could be identified from this data.

Arrays were incubated with 1 μg / ml and 10 μg / ml dilutions of MIL38-AM4 under normal stringency conditions. A concentration-dependent reaction was observed (FIGS. 3A and 3B). No saturation was observed at 10 μg / ml, indicating that none of the peptides were complete epitopes. Two non-adjacent reaction clusters within the primary structure were identified. The two common nuclei were ₁₃₅ TQNArafRD ₁₄₃ (SEQ ID NO: 7) and ₃₄₈ VNPQGPPGPEEK ₃₅₈ (SEQ ID NO: 2), and the latter section was found to be clearly predominant over the former.

Section ₃₄₈ VNPQGPPGPEEK ₃₅₈ (SEQ ID NO: 2) is a three-dimensional (3D) model obtained from the Protein Data Bank identification number (PBD ID) 4AD7 (http://www.ebi.ac.uk/pdbsum/4AD7). It was not resolved in another pdb coordinate file (4ACR, 4BWE) published in 4), and it was considered that this section was movable. Section ₁₃₅ TQNArafRD ₁₄₃ (SEQ ID NO: 7) is adjacent to this missing loop, as evidenced by the positions of V348 and G362 resolved in the 3D model.

Similar to the binding of MIL38-AM4 to peptides observed in this array, it is common to bind to incomplete mimetics that partially meet the requirements of the antibody. We have discontinuity consisting of a major portion contributed by the mobile loop ₃₄₈ VNPQGPPGPEEK ₃₅₈ (SEQ ID NO: 2) and a secondary portion contributed by the helix ₁₃₅ TQNArafRD ₁₄₃ (residue of SEQ ID NO: 7). Assume what is an epitope.

1.3. Summary and Discussion The purpose of this study was to map the epitope of mouse anti-human gripican 1 (MIL38-AM4). Experimental sets covering reference sequences with various conformational constraints were generated and the antibodies were probed with peptide arrays. Discontinuous epitope consisting of a major portion contributed by the mobile loop ₃₄₈ VNPQGPPGPEEK ₃₅₈ (SEQ ID NO: 2) and a secondary portion contributed by the helix ₁₃₅ TQNARAPPEEK ₁₄₃ (residue of SEQ ID NO: 7) from a significant binding. I could see the existence of.

Example 2: Identification and characterization of another glypican-1 epitope bound to another anti-glypican-1 antibody 2.1. Materials and Methods Table 8 below provides information on the antibodies used in this study. The first three of the antibodies listed are commercially available.

-Peptide A library of structured peptides was prepared using the human gripican-1 (GPC-1) sequence defined by SEQ ID NO: 14 as a base.

A rendered image of the chain B existing as Protein Data Bank identification number (PBD ID) 4AD7 (http://www.ebi.ac.uk/pdbsum/4AD7) is shown in FIG. 1A.

-Chemically Linked Peptides on Scaffolds (CLIPS) Technique The general principles of the CLIPS technique used in this experiment are described in Example 1 above.

-Peptide synthesis Peptide synthesis was performed using the method mentioned in Example 1. Chemically synthesized linear peptides and CLIPS peptides were synthesized according to the design (sets 1-5) shown in Example 1.

-ELISA screening Binding of the antibody to each synthetic peptide was tested with PEPSCAN-based ELISA as described in Example 1.

-Quality control of data processing and synthesis Data processing and synthesis quality control was carried out as in Example 1.

-Screening details Table 9 summarizes the antibody binding conditions. For Pepscan buffer and preparation (SQ), the numbers represent the relative amount of competing protein (combination of horse serum and ovalbumin). In addition, P / Tw (PBS-Tween) was used to reduce the binding stringency.

2.2 Results-Main experimental results and determination of signal-to-noise ratio Figure 5 graphs an overview of the entire dataset of untreated ELISA results obtained by screening. In this figure, a boxplot shows each dataset and represents the mean ELISA signal, distribution and outliers within each dataset. Various ELISA data distributions can be obtained depending on the experimental conditions (antibody amount, blocking intensity, etc.). From this data, epitopes of monoclonal and polyclonal sera could be identified, but those of MIL38-AM3 could not be identified.

-MIL38-AM3
MIL38-AM3 could not be detected even when tested at high concentrations (10 μg / ml) and low stringency (PBS-Tween). A different secondary antibody (sheep anti-mouse IgG HRP; GE Healthcare, NXA931) was also tried on the same sample, but no results were obtained either.

For confirmation, a direct ELISA was attempted to coat MIL38-AM3 on a plate. Antibodies could not be detected using rabbit anti-mouse IgG-HRP (Southern Biotech).

-Rabbit anti-glypican 1 / GPC1 antibody ab137604
As can be seen from the corresponding panel in FIG. 6, three major signals are seen in rabbit anti-GPC1. These signals correspond to sections ₃₄₈ VNPQGPGPEEK ₃₅₈ (SEQ ID NO: 2), ₃₆₆ PERRPP ₃₇₁ (SEQ ID NO: 10) and ₄₇₈ QDASDDGSGS ₄₈₇ (SEQ ID NO: 11).

-Mouse mAb2600 (Millipore)
Mouse antibody 2600 recognizes one distinct peak of all peptides having a common nucleus ₂₄₂ LGPECSRAVMK ₂₅₂ (SEQ ID NO: 13). This can be seen from the corresponding panel in FIG.

-Goat anti-GPC-1 (GPC1)
As can be seen from the corresponding panel in FIG. 6, two major signals are seen in the goat anti-GPC-1. These signals correspond to sections ₃₄₈ VNPQGPPGPEEK ₃₅₈ (SEQ ID NO: 2) and ₄₀₈ ALSTASDDR ₄₁₄ (SEQ ID NO: 9).

2.3 Summary and Discussion This study aims to characterize three commercially available anti-glypican 1 antibodies and additional mAbs (MIL38-AM3) in the same array. The antibody was probed with an existing peptide array as described in Example 1. Any commercially available anti-GPC-1 antibody could be mapped using the above array. The antibody MIL38-AM3 was found to be ineffective in mapping because it did not signal in any of the arrays due to the discontinuous properties of the epitope or the degradation of the sample.

Rabbit anti-GPC-1 recognizes at least three sections of glypican 1, namely ₃₄₈ VNPQGPGPEEK ₃₅₈ (SEQ ID NO: 2), ₃₆₆ PERRPP ₃₇₁ (SEQ ID NO: 10) and ₄₇₈ QDASDDGSGS ₄₈₇ (SEQ ID NO: 11). Two of these sections have the coordinate file 4AD7. As illustrated in FIG. 7A. It is resolved by pbd. Since it is a preparation of polyclonal antibodies, it is not possible to assess whether this epitope is linear or part of a complex epitope.

Mouse anti-glypican mab2600 recognizes section ₂₄₂ LGPECSRAVMK ₂₅₂ (SEQ ID NO: 13) of the entire peptide set of the array. Coordinate file 4AD 7. The location of the epitope on the pdb is shown in FIG. 7B.

Goat anti-glypican 1 recognizes at least two sections of glypican 1, namely ₃₄₈ VNPQGPGPEEK ₃₅₈ (SEQ ID NO: 2) and ₄₀₈ ARSTASSDR ₄₁₄ (SEQ ID NO: 9). Since it is a preparation of polyclonal antibodies, it is not possible to assess whether this epitope is linear or part of a complex epitope. Neither interval is resolved in the available coordinate files.

Both rabbit and goat polyclonal preparations recognize section ₃₄₈ VNPQGPPGPEEK ₃₅₈ (SEQ ID NO: 2) of glypican 1, which section forms part of the (presumably discontinuous) binding site of Mab MIL38-AM4. It is also a thing. Both polyclonal preparations also recognize other epitopes of glypican 1, but it is not possible to assess whether these epitopes form one discontinuous epitope or a manifestation of the polyclonal nature of the sample. Neither pAb recognizes interval ₁₃₅ TQNARA _{140, which} is believed to contribute to MIL38-AM4 binding.

Mouse Mab2600 recognizes an epitope that is not common to any of the other anti-GPC-1 antibodies tested so far.

Example 3: Identification and characterization of another glypican-1 epitope bound to another anti-glypican-1 antibody 3.1. Materials and Methods Table 10 below provides information on the antibodies used in this test. Three anti-glypican 1 antibodies used in the previous experiments described in Example 1 and / or Example 2 above were used, respectively.

-Peptide The human gripican-1 (GPC-1) sequence on which this test was based is defined by SEQ ID NO: 14. The following sequence of residues was used:
GPC1_residue number 344-366 GNPKVNPQGPPGPEEKRRRGKLAP (SEQ ID NO: 15)
GPC1_residue number 131-149 GELYTQNARAFRDLYSELR (SEQ ID NO: 16)

-Peptide synthesis Peptide synthesis was performed using the method mentioned in Example 1. Chemically synthesized linear and CLIPS peptides were synthesized according to the design shown below:

-ELISA screening Binding of the antibody to each synthetic peptide was tested with PEPSCAN-based ELISA as described in Example 1.

-Quality control of data processing and synthesis Data processing and synthesis quality control was carried out as in Example 1.

-Heatmap analysis A brief overview of the heatmap methodology used is given below.

A heat map is one of a graph display of data in which numerical values taken by variables in a two-dimensional map are represented by colors. In a two-dimensional loop CLIPS peptide, such a two-dimensional map can be derived from the independent sequences of the first and second loops. For example, a given set of 16 CLIPS peptide sequences is an efficient reordering of the four unique subsequences in Loop 1 and the four unique subsequences in Loop 2. Therefore, the data observed in the ELISA can be plotted in a 4x4 matrix, where the X coordinates each correspond to the array of the first loop and the Y coordinates each correspond to the array of the second loop. To do.

For easier visualization, the ELISA values can be replaced with continuous shading gradients. In this case, extremely low values are represented by bright colors, extremely high values are represented by dark colors, and average values are represented by black. Applying this gradient map to the Data Matrix gives a shaded heatmap.

-Screening details Table 11 summarizes the antibody binding conditions. For Pepscan buffer and preparation (SQ), the numbers represent the relative amount of competing protein (combination of horse serum and ovalbumin).

3.2. Results-Main experimental results and determination of signal-to-noise ratio An overview of the entire dataset of untreated ELISA results obtained by screening is graphed in FIG. In this figure, a boxplot shows each dataset and represents the mean ELISA signal, distribution and outliers within each dataset. Various ELISA data distributions can be obtained depending on the experimental conditions (antibody amount, blocking intensity, etc.).

-Rabbit polyclonalAb137604
In Example 2, it was found that section ₃₄₈ VNPQGPPGPEEK ₃₅₈ (SEQ ID NO: 2) was sufficient to bind some IgG from rabbit polyclonal Ab137604. In this test, any of the constructs containing ₃₄₈ VNPQGPGPEE ₃₅₇ (SEQ ID NO: 3) was similarly bound to 1/2500 diluted IgG from this sample. In the set 1 matrix, no signal enhancement is seen in any particular construct.

From the substitution analysis of FIG. 9, it can be seen that residues P353, G354 and E356 are essential. The possible substitutions at positions Q351, G352 and E357 are limited.

-Goat polyclonal anti-GPC-1
In Example 2, a section ₃₄₈ VNPQGPPGPEEK ₃₅₈ (SEQ ID NO: 2) was also sufficient to bind some IgG from goat polyclonal anti-GPC-1. This antibody recognizes the same loop as the rabbit polyclonal antibody, but with slightly different subtle specificities when recognizing it. In the character plot of FIG. 10, the most important residues are G352, G.
It can be seen that with 354 and E356, the possible substitutions at positions N349, Q351 and P353 are limited. Signal enhancement is seen in the set 1 matrix. The major mapping of this antibody did not show a section near residues 140-149, but another construct containing this section would be an excellent bait for binding some IgG in this polyclone.

-Antibody MIL38-AM4
In Examples 1 and 2, it was confirmed that MIL38-AM4 binds to the glypican section ₃₄₈ VNPQGPGPEEK ₃₅₈ (SEQ ID NO: 2) as well as section ₁₃₅ TQNARA ₁₄₀ (SEQ ID NO: 8), which indicates the presence of discontinuous epitopes. It was thought to indicate.

The looped construct containing this major interval pinpoints the most important residues for binding. From FIG. 10, it can be seen that the residues V348, Q351, G352 and P353 are not allowed to be substituted, K347, N349 and P350 are much more necessary and G354, P355 and E356 are less so.

Optimization of imitation recognition by MIL38-AM4 by adding residues in the range 135-143 to the main loop matrix of set 1.

Similarly, these series revealed the need for residues in and around V348. Other bindings were found in the matrix set, which ultimately provided the optimal signal for the T3 constrained CGELYTQNARAFRDLCGNPKVNPQGPPGPEEKRRRGC (SEQ ID NO: 12) (FIG. 12).

-Similarity and dissimilarity As can be seen from the scatter plot in FIG. 13, some antibodies bind to similar constructs and others do not. However, many constructs are recognized exclusively in one of the preparations (points along the axis or lower right and upper left).

-Conclusion The characteristics of the three-dimensional structure epitope of antibody MIL38-AM4 were clarified in a form supplementing Examples 1 and 2. It was found that the polyclonal antibodies AB137604 (rabbit) and anti-GPC-1 24-530 (goat) recognize similar epitopes. The two were compared and contrasted in the same array.

Matrix arrays with different loop lengths were made using the two reads obtained in Example 1 showing a discontinuous epitope for MIL38-AM4. In addition, total substitution analysis was performed on each read sequence. All arrays were probed with the above three antibodies.

With respect to the recognition of glypican 1, all antibodies examined in this study consist only of a mobile loop of residues 347-358 or bind to an epitope consisting primarily of this loop. However, the subtle specificities are different, which can affect their functional properties and thus their in vivo selectivity or applicability in identification tests.

The epitope of rabbit polyclonalAb137604 (some IgG species found in) is the linear section ₃₄₈ VNPQGPGPEE ₃₅₇ (SEQ ID NO: 3). There is no indication of the presence of an antibody that recognizes the three-dimensional structure epitope.

Goat polyclonal anti-GPC-1 (some IgG species found in) recognizes the same mobile loop. There is some preference for structured imitations, but not a great deal. It is also possible that not all antibodies in this preparation recognize mobile loops in the same way. The monoclonal antibody MIL38-AM4 primarily binds to the loop of residues 347-355 of glypican 1, but it is clear that the addition of residues in the range 135-143 to the peptide is effective for this antibody. The imitations produced are not yet optimal, which is due to the fact that 1000 times the concentration of antibody is required to obtain signal intensities comparable to those recorded in rabbit Ab137604. It is reflected and further indicates that there is more to be needed for the binding substrate.

This does not affect the affinity for the target protein that can be revealed by quantitative methods (eg, Biacore). In fact, sensitive selectivity does not guarantee the quality of antibodies that can be used in vivo without causing side effects.

Based on the results described above, Table 13 below summarizes the permutations allowed in the analyzed epitope sequences.

Example 4. Overlapping reactivity on two-dimensional Western blots is seen between the MIL38 antibody and the anti-glypican-1 (anti-GPC-1) antibody.
The rabbit anti-GPC-1 antibody ab137604 showed reactivity of glypican-1 with the core protein at a molecular weight of about 60 kDa (same as the molecular weight detected by MIL38). To support MIL38's recognition of glypican-1, MPEK extracts of prostate cancer DU-145 were subjected to two-dimensional electrophoresis and Western blotting.

Membrane protein extracts (MPEK) of DU-145 prostate cancer cells were separated on a two-dimensional gel (pI gradient horizontal, molecular weight vertical). Western blots using the MIL38 antibody and the commercially available rGPC-1 rabbit polyclonal antibody show overlapping reactivity showing 60 Kd protein (circled in FIG. 14). Lane D (FIG. 14) is a one-dimensional separation of the control DU-145 extract. Lane M (FIG. 14) is a control one-dimensional separation lane for the molecular size marker.

As can be seen from FIG. 14, the MIL38 antibody and the anti-GPC-1 antibody showed overlap in the reactivity of detecting a protein having a molecular weight of 60 kDa and an isoelectric point range of 5 to 7.

Example 5. MIL38 was detected in the immunoprecipitate of anti-GPC-1, and vice versa.
MIL38 antibody or rabbit anti-GPC-1 antibody was used to immunoprecipitate each antigen from the MPEK extract of DU-145 or C3 (MIL38 negative). The immunoprecipitate (IP) was subjected to Western blot with MIL38 antibody or anti-GPC-1 antibody (Fig. 15).

A 60 kDa GPC-1 reactive band was detected in the IP of MIL38 blotted with anti-GPC-1, and a 60 kDa MIL38 reactive band was detected in the IP of anti-GPC-1 blotted with MIL38. No reactivity was detected in the control with only the secondary antibody. Furthermore, immunoprecipitation with the MIL38 antibody almost completely depleted both the MIL38 antigen and the anti-GPC-1 antigen, strongly suggesting that the MIL38 antigen is glypican-1.

MIL38 antibody and rabbit anti-GPC-1 antibody were used to immunoprecipitate each antigen from DU-145 prostate cancer or C3 (MIL38 negative) cell membrane protein extract. Western blot of immunoprecipitation detected with MIL38 antibody or anti-GPC-1 antibody is shown. FIG. 15A shows GPC1 detection of MIL38 immunoprecipitate (left) and MIL38 detection of GPC1 immunoprecipitation (right). FIG. 15B shows MIL38 detection of a control MIL38 immunoprecipitate. Each lane is a control Magic Mark-commercial protein marker; DU145 MPEK-prostate cancer membrane protein extract (not immunoprecipitated); DU145 FT-prostate cancer flow-through obtained by immunoprecipitation; DU145
Immunoprecipitation with IP-antibodies; C3 MPEK- (MIL38 negative) control membrane protein extract (not immunoprecipitated); flow-through obtained by C3 FT-immunoprecipitation; C3
IP Eluate-An immunoprecipitate using an antibody (MIL38 negative). MIL38 can detect immunoprecipitates due to rGPC1 antibody and vice versa. MIL38 can also be combined with all controls including DU145 MPEK and the IP obtained by MIL38.

Example 6. GPC-1 can be detected by MIL38 contained in prostate cancer plasma samples and membrane extracts of prostate cancer patients.
Plasma samples from one normal patient (042) and one prostate cancer patient (046) were immunoprecipitated with MIL38 antibody and IP samples were subjected to Western blot with MIL38 antibody and anti-GPC-1 antibody (FIG. 16A).

Both antibodies detected a specific band of about 70 kDa in both plasma samples. Both the MIL38 antibody and the anti-GPC-1 antibody have a significantly higher signal (darker band) in the plasma of prostate cancer patients than in the plasma of normal patients, and this soluble glypican-1 is increased in prostate cancer patients. It was suggested that there is a possibility of doing so.

One sample each was obtained from Novus Bio to determine if the MIL38 antigen could be detected in normal prostate and prostate cancer membrane protein extracts. Western blotting was performed on equal amounts of protein using MIL38 antibody (Fig. 16B). It was found that the expression of MIL38 antigen was much higher in the prostate cancer extract than in the normal prostate sample.

Example 7. Detection of MIL38 antigen in patient urine.
MIL38 can detect cells in the urine of prostate cancer patients. To test the sensitivity and specificity of this detection method, 125 age-matched urine samples were obtained. Cells were precipitated from urine and analyzed by direct immunofluorescence assay using MIL38. A total of 47 healthy controls, 37 benign prostatic hyperplasia (BPH) and 41 biopsy-confirmed prostate cancers were analyzed.

Testing by immunofluorescence assay (IFA) with MIL38 revealed that the sensitivity and specificity of prostate cancer discrimination within the cohort was 71%. The study found that prostate cancer discrimination sensitivity to BPH patients was 71% and specificity was 76% (Table 14).

Claims (51)

An epitope of an anti-glypican 1 (GPC-1) antibody located within a portion of the GPC-1 mobile loop defined by the amino acid sequence KVNPQGPPGPEEK (SEQ ID NO: 1). (I) VNPQGPPGPEEK (SEQ ID NO: 2); or (ii) a variant of VNPQGPPGPEEK (SEQ ID NO: 2).
(A) One or more positions of 2nd, 3rd, 7th, 8th, 9th, 10th and / or 11th; or (b) 1st, 2nd, 3rd, One or more of the 4th, 6th, 8th, 10th and / or 11th positions; or (c) 1st, 2nd, 3rd, 4th, 5th, 8th, The epitope according to claim 1, wherein the epitope comprises a first segment containing an amino acid sequence selected from a variant containing a substituted amino acid residue only at any one or more positions of the 10-position and / or 11-position. .. (I) KVNPQGPGP (SEQ ID NO: 6); or (ii) KVNPQGPGP (SEQ ID NO: 6) substituted amino acids only at one or more of the 1st, 3rd, 4th, 8th and 9th positions. The epitope of claim 1, comprising a first segment comprising an amino acid sequence selected from the variant of SEQ ID NO: 6, comprising a residue. The variant according to claim 3, wherein the variant comprises a substituted amino acid residue only at one or more of positions 8 and 9 of SEQ ID NO: 6. (I) KVNPQGPGPE (SEQ ID NO: 5); or (ii) KVNPQGPPGPE (SEQ ID NO: 5) at one or more of the 1st, 3rd, 4th, 8th, 9th and 10th positions. The epitope of claim 1, comprising a first segment comprising an amino acid sequence selected from the variant of SEQ ID NO: 5, containing only a substituted amino acid residue. The variant according to claim 5, wherein the variant comprises a substituted amino acid residue only at any one or more of positions 8, 9, and 10 of SEQ ID NO: 6. The variant according to claim 5 or 6, wherein the E (glu) at position 10 is replaced with any other amino acid. 1st place where K (lys) is replaced with any one of W (trp), R (arg), L (lys), Y (tyr) or F (phe);
The third position where N (asn) is replaced with any one of H (his), P (pro) or D (asp);
4th place where P (pro) is replaced by any one of R (arg), K (lys), W (trp), S (ser), H (his) or N (asn);
G (gly) is replaced with any one of D (asp), E (glu), N (asn), Q (gln), K (lys), R (arg) or A (ala) 8 Rank;
P (pro) is M (met), A (ala), I (ile), K (lys), R (ar)
g), Q (gln), S (ser), T (thr) or Y (tyr) is substituted at any one or more of the 9 positions. , The mutant according to any one of claims 3 to 7. The epitope of any one of claims 1-8, comprising a second segment comprising the amino acid sequence TQNARA (SEQ ID NO: 8). The epitope of any one of claims 1-8, comprising a second segment comprising the amino acid sequence TQNARAFRD (SEQ ID NO: 7). (I) NPQGPPGPEE (SEQ ID NO: 4); or (ii) at one or more of the 1st, 2nd, 3rd, 5th, 7th and 9th positions of NPQGPGPEE (SEQ ID NO: 4). The epitope according to claim 1 or 2, comprising a first segment comprising an amino acid sequence selected from the variant of SEQ ID NO: 4, which comprises only a substituted amino acid residue. The variant of claim 11, wherein the variant comprises a substituted amino acid residue only at any one or more of positions 2, 7, and 9 of SEQ ID NO: 4. 1st place where N (asn) is replaced by H (his);
2nd position where P (pro) is replaced with any other amino acid;
The third position where Q (gln) is replaced with any one of N (asn), M (met), T (thr), S (ser) or R (arg);
5th place where P (pro) is replaced by A (ala);
P (pro) is A (ala), D (asp), C (cys), E (glu), Z (glx), G (gly), H (his), K (lys), M (met), 7th position substituted with any one of F (phe), P (pro), S (ser), T (thr), W (trp) or Y (tyr);
The variant according to claim 11 or 12, wherein E (glu) comprises a substitution at any one or more positions of the 9-position substituted with any other amino acid. The epitope of any one of claims 11-13, comprising a second segment comprising the amino acid sequence ALSTASDDR (SEQ ID NO: 9). (I) VNPQGPPGPEE (SEQ ID NO: 3); or (ii) one or more of the 1st, 2nd, 3rd, 4th, 5th, 8th and 10th positions of VNPQGPGPEE (SEQ ID NO: 3). The epitope of claim 1 or 2, comprising a first segment comprising an amino acid sequence selected from the variant of SEQ ID NO: 3, comprising a substituted amino acid residue only in position. 15. The variant of claim 15, wherein the variant comprises a substituted amino acid residue only at any one or more of positions 1, 2, 3, and 8 of SEQ ID NO: 3. Position 1 where V (val) is replaced with any other amino acid;
2nd position where N (asn) is replaced with any other amino acid;
Position 3 where P (pro) is replaced with any other amino acid;
Q (gln) is Y (tyr), A (ala), E (glu), V (val), M (met), F (phe), L (leu), I (ile), T (thr) or 4th place replaced by any one of R (arg);
G (glyc) is any one of A (ala), S (ser), T (thr), H (his), W (trp), Y (tyr), F (phe) or M (met). Substituted 5th place;
Position 8 where P (pro) is replaced with any other amino acid;
Replace with one or more of the 10 positions where E (glu) is replaced with Q (gln), D (asp), F (phe), H (his) or M (met). The variant according to claim 15 or 16, which comprises. Amino acid sequence PERRPP (SEQ ID NO: 10) or amino acid sequence QDASSDDGSGS (SEQ ID NO: 11)
The epitope of any one of claims 15-17, comprising a second segment comprising. The epitope according to any one of claims 15 to 17, which comprises a second segment containing the amino acid sequence PERRPP (SEQ ID NO: 10) and a third segment containing the amino acid sequence QDASSDDGSGS (SEQ ID NO: 11). The epitope according to any one of claims 1 to 10, which comprises the amino acid sequence CGELYTQNARAFRDLCGNPKVNPQGPPGPEEKRRRGC (SEQ ID NO: 12). The epitope according to any one of claims 1 to 20, which is a linear epitope. 19. The epitope of claim 19, wherein the second segment and the third segment of the epitope are discontinuous. The epitope according to any one of claims 9, 10, 14, 18 or 22, wherein the first segment and the second segment of the epitope are discontinuous. Select from one or more of TQNARA (SEQ ID NO: 8), ALSTASDDR (SEQ ID NO: 9), PSERPP (SEQ ID NO: 10), QDASDDGSGS (SEQ ID NO: 11), LGPECSRAVMK (SEQ ID NO: 13) and TQNARAFRD (SEQ ID NO: 7). An epitope of an anti-glypican 1 (GPC-1) antibody comprising the amino acid sequence to be used. The epitope according to any one of claims 1 to 24, which is an isolated polypeptide or a synthetic polypeptide. A combination of epitopes comprising a combination of two or more different epitopes, wherein the different epitopes are respectively the epitope according to any one of claims 1-25. Contains a combination of two or more different epitopes
The first epitope according to any one of claims 1 to 10 and
The second epitope according to any one of claims 11 to 14 is included.
Assortment of epitopes. Contains a combination of two or more different epitopes
The first epitope according to any one of claims 1 to 10 and
The second epitope according to any one of claims 15 to 19 is included.
Assortment of epitopes. A composition comprising the epitope according to any one of claims 1 to 25 or the combination of the epitope according to any one of claims 26 to 28 and a pharmaceutically acceptable carrier or excipient. .. An assembly comprising the combination of the epitope according to any one of claims 1 to 25 or the epitope according to any one of claims 26 to 28 bound to one or more soluble or insoluble supports. body. The aggregate according to claim 30, which is a component of an enzyme-linked immunosorbent assay (ELISA). A nucleic acid encoding the epitope according to any one of claims 1 to 25. A vector comprising the nucleic acid of claim 32. A host cell comprising the vector according to claim 33. An isolated binding entity capable of specifically binding to the epitope according to any one of claims 1 to 25, which is not an antibody. An isolated binding entity capable of specifically binding to the epitope according to any one of claims 1 to 25, which is an antibody, wherein the antibody is a MIL38 antibody (CBA20140026), rabbit. A binding entity that is not an anti-GPC-1 polyclonal antibody (ab137604, abcam), a mouse anti-glypican monoclonal antibody 2600 clone 4D1 (Millipore) or a goat anti-glypican 1 antibody (AA24-530). A method for detecting prostate cancer of a subject, wherein a biological sample is collected from the subject, and the presence of the epitope according to any one of claims 1 to 25 is detected in the sample. A method comprising determining that the subject has or is likely to develop prostate cancer based on the amount of the epitope detected in the sample. Detecting the presence of an epitope in the sample comprises contacting the sample with a binding entity capable of specifically binding to the epitope according to any one of claims 1-25. 37. The method of claim 37. 38. The method of claim 38, wherein the binding entity is a population of antibodies. The group of antibodies is MIL38 antibody (CBA20140026), rabbit anti-GPC-1 polyclonal antibody (ab137604, abcam), mouse anti-glypican monoclonal antibody 2600 clone 4D1 (Millipore) or goat anti-glypican 1 antibody (AA24-530). 39. The method of claim 39, comprising any one or more of the above. The group of antibodies includes MIL38 antibody (CBA20140026), rabbit anti-GPC-1 polyclonal antibody (ab137604, abcam), mouse anti-glypican monoclonal antibody 2600 clone 4D1 (Millipore) or goat anti-glypican 1.
39. The method of claim 39, which comprises none of the antibodies (AA24-530). It involves comparing the amount of epitopes present in the biological sample with the amount of epitopes present in the control sample, and detects that the amount of epitopes in the body fluid sample is greater than the same measurement of the control sample. The method of any one of claims 37-41, where it indicates that the subject has prostate cancer or is likely to develop prostate cancer in the subject. 42. The method of claim 42, wherein the amount of epitopes detected in the sample is more than 50% greater than the amount of epitopes detected in the control sample. 17. the method of. Detecting the presence of the epitope includes or comprises the sample and the amino acid sequences defined by positions 48-58 of SEQ ID NO: 20. Complementarity determining regions 1 (CDR1); Complementarity determining regions 2 (CDR2) containing or consisting of the amino acid sequence defined by position 80; and complementarity determining regions 3 (CDR3) containing or consisting of the amino acid sequences defined by positions 113 to 121 of SEQ ID NO: 20. The method of any one of claims 37-43, comprising contacting with a population of anti-glypican 1 antibodies that does not contain antibodies that contain light chain variable regions. The invention according to any one of claims 37 to 45, further comprising determining the level of prostate-specific antigen (PSA) in the biological sample and comparing the detected level with that of the control sample. the method of. The method according to any one of claims 37 to 46, wherein the biological sample is a body fluid sample. The method according to any one of claims 37 to 46, wherein the biological sample is a tissue sample. A fusion protein comprising the epitope according to any one of claims 1 to 25. The epitope according to any one of claims 1 to 25, the combination of the epitope according to any one of claims 26 to 28, or the combination of the epitope according to claim 48 as a positive control element of the method for detecting GPC-1. Use of fusion proteins. The use according to claim 50, wherein the method is the method for detecting prostate cancer according to any one of claims 37 to 48.