CA3105726A1 - Bcl-2 antibodies and immunoassay for diagnosis of cancer - Google Patents

Abstract

The present invention is directed to a monoclonal antibody that recognizes human BCL-2 in its native form. The invention is also directed to a hybridoma cell line that produces the monoclonal antibody, and to immunoassays such as ELISA and Lateral flow Assay tests for quantifying the quantity of BCL-2 for diagnosing cancer.

Description

BC1-2 Antibodies and Immunoassay for Diagnosis of Cancer Priority and Incorporation by Reference [001] This application claims priority to United States Provisional Application 62/694,142 filed on July 5, 2018. All references cited herein are expressly incorporated by reference.
Background

[002] The use of BCL-2 as a cancer marker is described in U.S. patent 8,034,549 and published patent applications US 2011-0318763 Al and US 2016-0258960 Al. While these references teach antibodies to BCL-2, an antibody meeting regulatory manufacturing requirements and having improved specificity was required.

[003] There are several anti-BCL-2 monoclonal antibodies described in the literature, however, a need exists for new anti-BCL-2 antibodies having unique genetic and amino acid structures, including unique binding and functional characteristics.
Brief Description of the Invention

[004] The present invention is directed to antibodies and fragments thereof that bind to human BCL-2. The antibodies may be labeled with one or more labels selected from the group consisting of a biotin label, a fluorescent label, an enzyme label, a coenzyme label, a chemiluminescent label, colloidal particles, and a radioactive isotope label.

[005] The invention is also directed to a hybridoma cell line that produces the antibody, and to methods of treating cancer and purifying exosomes using the antibody or antigen-binding fragments thereof.

[006] The present invention is also directed to a method for diagnosing cancer, wherein the method comprises: reacting an anti- BCL-2 antibody with a sample collected from the subject; detecting an BCL-2 protein in the sample; and diagnosing cancer when the level of BCL-2 protein is higher in the sample than in a normal sample, wherein the sample collected from the subject is at least one clinical sample selected from the group consisting of a urine sample, saliva sample, tissue sample, a blood sample, a serum sample, a plasma sample, tears, or a mucous sample.

[007] The antibodies of the present invention are preferably isolated monoclonal antibodies having specific binding properties against a human BCL-2 protein, more preferably against human BCL-2 in its native form.

[008] The invention is also directed to anti- BCL-2 antibody based immunoassays for detecting ovarian cancer.
Description of the Figures

[009] Figure 1 Human Bc1-2 Sequence & secondary structure prediction

[010] Figure 2: Homology of BCL-2 and BCL-x:

[011] Figure 3: Homology of Human and Mouse Bc1-2.

[012] Figure 4 shows the alignment of epitopes to Bc1-2.

[013] Figure 5A-C: Structural predictions of Bc1-2 binding sites.

[014] Figure 6 is an electropherogram of a Bc1-2 antibody of the present invention.

[015] Figure 7 is an electropherogram of a Bc1-2 antibody of the present invention.

[016] Figure 8 is an image of an electrophoresis gel of a Bc1-2 antibody of the present invention.

[017] Figure 9 is a chromatograph of a Bc1-2 antibody of the present invention.

[018] Figure 10 is an isoelectric gel of a Bc1-2 antibody of the present invention.

[019] Figure 11 is an image of an electrophoresis gel of a Bc1-2 antibody of the present invention.

[020] Figure 12 is a chromatograph of a Bc1-2 antibody of the present invention.

[021] Figure 13 is an isoelectric gel of a Bc1-2 antibody of the present invention.

[022] Figure 14 is an image of an electrophoresis gel of a Bc1-2 antibody of the present invention.

[023] Figure 15 is an isoelectric gel of a Bc1-2 antibody of the present invention.

[024] Figure 16 is a chromatograph of a Bc1-2 antibody of the present invention.

[025] Figure 17 is an image of an electrophoresis gel of a Bc1-2 antibody of the present invention.

[026] Figure 18 is a chromatograph of a Bc1-2 antibody of the present invention.

[027] Figure 19 is an isoelectric gel of a Bc1-2 antibody of the present invention.

[028] Figure 20 is an image of an electrophoresis gel of a Bc1-2 antibody of the present invention.

[029] Figure 21 is an isoelectric gel of a Bc1-2 antibody of the present invention.

[030] Figure 22 is a chromatograph of a Bc1-2 antibody of the present invention.

[031] Figure 23 is a graph showing absorbance of antibodies of the present invention.

[032] Figure 24 is a DNA amino acid alignment for Clone 10Al2 Heavy Chain

[033] Figure 25 DNA is a DNA amino acid alignment for Clone 10Al2 Light Chain

[034] Figure 26 DNA is a DNA amino acid alignment for Clone 14A09 Heavy Chain

[035] Figure 27 DNA is a DNA amino acid alignment Clone 14A09 Light Chain

[036] Figure 28 is a photograph of a lateral flow assay.

[037] Figure 29 is a photograph of a lateral flow assay.

[038] Figure 30 is a photograph of a lateral flow assay.

[039] Figure 31 is a photograph of a lateral flow assay.

[040] Figure 32 is a photograph of a lateral flow assay.

[041] Figure 33 is a photograph of a lateral flow assay.

[042] Figure 34 is a photograph of a lateral flow assay.

[043] Figure 35 is a photograph of a lateral flow assay.

[044] Figure 36 is a photograph of a lateral flow assay.

[045] Figure 37 is a photograph of the lateral flow assay in a cassette.
Detailed Description of the Invention

[046] The present invention is directed to antibodies and fragments thereof that bind to human BCL-2. The antibodies may be labeled with one or more labels selected from the group consisting of a biotin label, a fluorescent label, an enzyme label, a coenzyme label, a chemiluminescent label, colloidal particles, and a radioactive isotope label.

[047] The invention is also directed to a hybridoma cell line that produces the antibody, and to methods of treating cancer and purifying exosomes using the antibody or antigen-binding fragments thereof.

[048] The present invention is also directed to a method for diagnosing cancer, wherein the method comprises: reacting an anti- BCL-2 antibody with a sample collected from the subject; detecting an BCL-2 protein in the sample; and diagnosing cancer when the level of BCL-2 protein is higher in the sample than in a normal sample, wherein the sample collected from the subject is at least one sample selected from the group consisting of a tissue sample, a urine sample, a saliva sample, a blood sample, a serum sample, and a plasma sample.

[049] The antibodies of the present invention are preferably isolated monoclonal antibodies having specific binding properties against a human BCL-2 protein, more preferably against human BCL-2 in its native form.

[050] In one form the invention comprises an ELISA in which a first antibody binds to Bc1-2 anchoring it to a substrate and a second antibody is labelled for identification. The label is typically selected from a biotin label, a fluorescent label, an enzyme label, a coenzyme label, a chemiluminescent label, colloidal particles, and a radioactive isotope label.

[051] The term "antibody" as used herein refers to any naturally occurring antibody or antigen-binding protein, the production of which is induced by an immune system (immunoglobulins or IgGs). "Conventional" antibodies comprise two heavy chains linked together by disulfide bonds and two light chains, one light chain being linked to each of the heavy chains by disulfide bonds. Each heavy chain has at one end a variable domain (VH) followed by a number of constant domains (three or four constant domains, CHL CH2, CH3 and CH4, depending on the antibody class). Each light chain has a variable domain (VL) at one end and a constant domain (CL) at its other end; the constant domains of the light chains each align with the first constant domains of the heavy chains, and the light chain variable domains each align with the variable domains of the heavy chains. This type of antibodies exist in camels, dromedaries and llamas along with an "unconventional" naturally occurring type of antibodies consisting of only two heavy chains, and thus being devoid of light chains. Other "unconventional"
naturally occurring antibodies exist in in the serum of nurse sharks (Ginglymostomatidae) and wobbegong sharks (Orectolobidae). These latter antibodies are called Ig new antigen receptors (IgNARs). They are disulfide-bonded homodimers consisting of five constant domains (CNAR) and one variable domain (VNAR).
There is no light chain, and the individual variable domains are independent in solution and do not appear to associate across a hydrophobic interface (Greenberg et al.
1995, Nature 374, 168-173; Nuttall et al. 2001, Mol Immunol 38, 313-326; Diaz et al. 2002, Immunogenetics 54, 501-512; Nuttall et al. 2003, Eur J Biochem 270, 3543-3554). Due to the heavy chain dimer structure characteristic of camelid and shark antibodies, these are sometimes termed "Heavy-Chain Mini-Antibodies" (mnHCAbs) or simply "Mini-Antibodies" (mnAbs) (Holliger & Hudson 2005, Nature Biotechnol 23, 1126-1136).

The complementary determining region 3 (CDR3) of camel antibodies and shark antibodies is usually longer (comprising about 16-21 amino acids, and about 16-amino acids, respectively) than the CDR3 of mouse VH region (comprising about amino acids) (Muyldermans et al. 1994, Prot Eng 7, 1129-1135; Dooley & Flajnik 2005, Eur J Immunol 35, 936-945). Without the light chain, these heavy-chain antibodies bind to their antigens by one single domain, the variable antigen binding domain of the heavy-chain immunoglobulin, referred to as Vab (camelid antibodies) or V-NAR
(shark antibodies). These smallest intact and independently functional antigen-binding fragment Vab is referred to as nano-antibody or nanobody (Muyldermans 2001, J
Biotechnol 74, 277-302). Multivalent (etc. divalent, trivalent, tetravalent and pentavalent) Vab and/or V-NAR domains may be preferred in some instances due to their potentially higher cellular intake and retention and may be made by recombinant technology or by chemical means, such as described in WO 2010/033913. The variable domains of the light and/or heavy chains are involved directly in binding the antibody to the antigen. The variable domains of naturally occurring light and heavy chains have the same general structure: four framework regions (FRs) connected by three complementarity determining regions (CDRs) (see e.g. Kabat et al. 1991, Sequences of Proteins of Immunological Interest, 5^th Ed. Public Health Service, National Institutes of Health, Bethesda, Md.). The CDRs in a light or heavy chain are held in close proximity by the FRs and contribute to the formation of the antigen binding site.
The term "antibody fragment" refers to any molecule comprising one or more fragments (usually one or more CDRs) of an antibody (the parent antibody) such that it binds to the same antigen to which the parent antibody binds. Antibody fragments include Fv, Fab, Fab', Fab'-SH, single-chain antibody molecules (such as scFv), F(ab')₂, single variable VH domains, and single variable VL domains (Holliger & Hudson 2005, Nature Biotechnol 23, 1126-1136). The term further includes microantibodies, i.e. the minimum recognition unit of a parent antibody usually comprising just one CDR
(Heap et al. 2005, J Gen Virol 86, 1791-1800). Any of the fragments can be incorporated in a multivalent and/or multispecific larger molecule, e.g. mono- or bispecific Fab₂, mono- or tri-specific Fab₃, bis-scFv (mono- or bispecific), diabodies (mono- or bispecific), triabodies (e.g. trivalent monospecific), tetrabodies (e.g.
tetravalent monospecific), minibodies and the like (Holliger & Hudson 2005, Nature Biotechnol 23, 1126-1136). Any of the fragments can further be incorporated in e.g. V-NAR

domains of shark antibodies or VhH domains of camelid antibodies (nanobodies).
All these are included in the term "antibody fragment".

[052] The term "monoclonal antibody" refers to a population of substantially homogeneous antibodies. In contrast to polyclonal antibody preparations that typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. The modifier "monoclonal" is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler & Milstein 1975, Nature 256, 495-497), or may be made by recombinant DNA
methods (e.g. U.S. Pat. No. 4,816,567). Monoclonal antibodies may also be isolated from phage antibody libraries using the techniques described in, e.g., Clackson et al.
1991, Nature 352, 624-628 or Marks et al. 1991, J Mol Biol 222, 581-597, or by yet other techniques or technologies.

[053] In the hybridoma method, a mouse or other appropriate host animal, such as a hamster or macaque monkey, is immunized to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the protein used for immunization (Harlow & Lane; Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y. (1988).

[054] The present invention also encompasses nucleic acid molecules encoding antibodies of the invention. In some embodiments, different nucleic acid molecules encode a heavy chain variable region and a light chain variable region of an antigen-specific antibody.
In other embodiments, the same nucleic acid molecule encodes a heavy chain and a light chain variable regions of an antigen-specific antibody.

[055] DNA encoding a monoclonal antibody of the invention may be isolated and sequenced from a hybridoma cell secreting the antibody using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the monoclonal antibodies). Sequence determination will generally require isolation of at least a portion of the gene or cDNA of interest. Usually this requires cloning the DNA or, preferably, mRNA (i.e., cDNA) encoding the monoclonal antibodies. Cloning is carried out using standard techniques (see, e.g., Sambrook et al. (1989) Molecular Cloning: A Laboratory Guide, Vols 1-3, Cold Spring Harbor Press, which is incorporated herein by reference). For example, a cDNA
library may be constructed by reverse transcription of polyA+ mRNA, preferably membrane-associated mRNA, and the library screened using probes specific for human immunoglobulin polypeptide gene sequences. Nucleotide probe reactions and other nucleotide hybridization reactions are carried out at conditions enabling the identification of polynucleotides which hybridize to each other under specified conditions.

[056] One exemplary set of conditions is as follows: stringent hybridization at 42 C. in 50%
formamide, 5 times saline sodium citrate "5 SC", 20 mM Na.PO4, pH 6.8; and washing in 1xSSC at 55 C for 30 minutes. Formula for calculating equivalent hybridization conditions and/or selecting other conditions to achieve a desired level of stringency are well known. It is understood in the art that conditions of equivalent stringency can be achieved through variation of temperature and buffer, or salt concentration as described Ausubel, et al. (Eds.), Protocols in Molecular Biology, John Wiley & Sons (1994), pp.
6Ø3 to 6.4.10. Modifications in hybridization conditions can be empirically determined or precisely calculated based on the length and the percentage of guanosine/cytosine (GC) base pairing of the probe. The hybridization conditions can be calculated as described in Sambrook, et al., (Eds.), Molecular Cloning: A
Laboratory Manual, Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y. (1989), pp.
9.47 to 9.51 The immunoassay of the present invention can be used with any suitable clinical specimen. Preferred specimens include urine, saliva, blood, serum, and plasma.
The specimens are collected and processed in conventional ways before tested using the immunoassay of the present invention.
Example 1: Human BCL-2 Antigenicity Determination

[057] The challenge was to produce a matched pair of monoclonal antibodies to the human BCL-2 protein that will work in a sandwich ELISA format. To accomplish this, peptides were be designed as antigens to regions with a high likelihood of generating specificity to the BCL-2 protein, but not cross react with BCL-x.

[058] Bioinformatic tools were used to analyze the protein as well as try to predict the best options for choosing peptides to be developed as antigens for the hybridoma projects.
It should be noted that this analysis is a computational prediction and is valuable in assisting in the decision process, however, these predictions are in no way considered guarantees for success of each individual project or the overall stated goal.
Human BCL-2 Sequence & secondary structure prediction:

[059] The secondary structure is presented graphically in Figure 1. Alpha helical predictions are shown by pink cylinders, beta strands by yellow arrows, and turns by blue arrows. Unstructured or loop regions are shown by grey squiggly lines.

Homology of BCL-2 & BCL-x:

[060] Referring to Figure 2, overall the homology of BCL-2 with BCL-x is 41%.
However, there are several structural domains that are conserved between the two proteins and the structural homology may be higher than is predicted by the sequence homology.
Of note are two regions that are quite dissimilar between the two: region 30-100 (BCL-2 sequence) & 205-241. The region between these two areas are quite conserved at both the sequence and structural level, therefore these two non-homologous regions would likely be the most appropriate regions to develop antibodies that target and are not cross reactive with BCL-x.
Homology of Human and Mouse BCL-2:

[061] Since the monoclonal antibodies are going to be generated in mouse, the similarity of the human and mouse BCL-2 protein needs to be considered. Referring to Figure 3, the overall homology is 90% between the two species, however there is a region between residues 35 and 81 that shows the highest level of divergence. With the exception of aa 99, the remainder of the protein is 100% identical. Therefore the most likely region for antibody generation would be in this area.
Linear Epitope Prediction:

[062] To predict areas that might be antigenic and therefore be good targets for antibody generation, analysis of potential epitopes was done using two methods that predict linear epitopes based on the sequence of the protein. This can be useful in identifying specific peptides to use for immunization. The results are shown in the Table 1 below and those that fall within the region of non-homology (between mouse & human) are highlighted in yellow.

[063] Table 1 KT Analysis No Start End Sequence Length 1 15 26 VMKYIHYKL SQR(SEQ ID NO 1) 2 35 52 VGAAPPGAAPAPGIFSSQ (SEQ ID NO 2) VVHLTLR (SEQ ID NO 3) 4 116 124 SSQLHLTPF (SEQ ID NO 4) 130 137 FATVVEEL (SEQ ID NO 5) 8 6 145 151 GRIVAFF (SEQ ID NO 6) 7 7 155 162 GVMCVESV (SEQ ID NO 7) 8 8 167 173 SPLVDNI (SEQ ID NO 8) 7 196 204 DAFVELYGP (SEQ ID NO 9) 9 BiPred Analysis 1 3 11 HAGRTGYDN (SEQ ID NO 10) 9 DPVARTSPLQTPAAPGAAAGPALSPVP (SEQ ID NO 11) 3 100 106 AGDDF SR (SEQ ID NO 12) 7 4 190 196 QDNGGWD (SEQ ID NO 13) 7 Example 2: Hybridoma Development

[064] Generation of Antigens

[065] A C terminus 10X His BCL-2 fragment HuBc1-2 10x His pET303 was generated in BL21 (DE3) E.coli and the resultant protein purified on Immobilized Metal Affinity Chromatography = IMAC (RL/P0003). 20mM Sodium Phosphate, 500mM NaC1 pH 7.4 w/ 40mM Imidazole, 20% Glycerol & 2mM DTT was used for binding and 20mM Sodium Phosphate, 500mM NaCl, pH 7.4, 500mM Imidazole, 20% Glycerol &
2mM DTT was used for elution. 5.2 gm of protein were recovered and reconstituted in 20mM Tris pH 7.5,100mM NaCl, 10% Glycerol, & 5mM DTT, 2mM EDTA at a final concentration: 0.7 mg/mL in a final volume of 7.5 mL. Referring to Figure 6, purity was determined to be greater than 95% as determined by Experion Pro260 Automated Electrophoresis. Molecular weight was approximately 26 KD. The process was repeated a second time and yielded a purity of 99%. See Figure 7.
Hybridoma 1

[066] Antibodies were generated using C57BL mice and hybridomas were created.
MBS
Accession: 15-0264RB2 for Cell Line: Bc1-2-41 Pep-KLH-BA-1.3-17D07-02D12 was conjugated with biotin and molar ratio quantified with (4'-hydroxyazobenzene-2-carboxylic acid) ("HABN") avidin assay which determined that 3.5 molecules of biotin per conjugated antibody from this hybridoma. Antibodies were purified using protein A affinity chromatography with a binding buffer of 0.5M NaCl in 0.1M
Citrate/Phosphate buffer, pH=9.0 and an elution buffer of 0.1M
citrate/phosphate , 0.15M NaCl, pH=3Ø The antibody eluted along a linear gradient with a pH
range of elution from 4.7-3.3. See Figure 8. 28.3mg antibodies were produced.

[067] Referring to Figure 9 purity was determined to be 100 percent using size exclusion chromatography. Referring to Figure 10, the isoelectric point was determined to be around 7.8 using 20 1 per well with a focusing conditions of 100v for 1 hour, 250v for 1 hour and 500v for 30 minutes.
Hybridorna 2

[068] Antibodies were generated using C57BL mice and hy bridomas were created.
MBS
Accession: 15-0264RE31 for Cell :Line: Bc1-2-41 Pep-KLH-BA-1.3-10Al2-02F02 was conjugated with biotin and molar ratio quantified with HABN avidin assay which determined that 6.2 molecules of biotin per conjugated antibody from this hybridoma. Antibodies were purified using protein A affinity chromatography with a binding buffer of 0.5M NaC1 in 0.1M Citrate/Phosphate buffer, pH=9.0 and an elution buffer of 0.1M citrate/phosphate, 0.15M NaC1, pH=3Ø The antibody eluted along a linear gradient with a p1-1 range of elution from 6.2-3.9. See Figure 11. 33.0 mg of antibody were recovered.

[069] Referring to Figure 12 purity was determined to be 100 percent using size exclusion chromatography. Referring to Figure 13, the isoelectric point was determined to be around 6.7 using 20g1 per well with a focusing conditions of 100v for 1 hour, 250v for] hour and 500v for 30 minutes.
Hybridoma 3

[070] Antibodies were generated using C57RL mice and hybridomas were created.
MBS
Accession: 15-0271 RBI for Cell Line: Bc1-2-61 Pep-KLH-BA-1.1-1 8E10-02G02 was conjugated with biotin and molar ratio quantified with HABN avidin assay which determined that 6.2 molecules of biotin per conjugated antibody from this hybridoma. Anti bodies were purified using protein A affinity chromatography with a binding buffer of 0.5M NaC1 in 0.1M Citrate/Phosphate buffer, pH=9.0 and an elution buffer of 0.1M citrate/phosphate, 0.15M: NaC1, pH=3Ø The antibody eluted along a linear gradient with a pH range of elution from 6.7-4.6. See Figure 14. 33.0 mg of antibody were recovered.

[071] Referring to Figure 15 purity was determined to be 100 percent using size exclusion chromatography. Referring to Figure 16, the isoelectric point was determined to be around 6.7 using 20111 per well with a focusing conditions of 100v for 1 hour, 250v for 1 hour and 500v for 30 minutes.

Hybridoma 4

[072] Antibodies were generated using C57131_, mice and hybridomas were created. MBS
Accession: 15-0271RB2 for Cell Line: Bc1-2-61 Pep-KLH-BA-1. 1-02C10-02D02-02B07 was conjugated with biotin and molar ratio quantified with HABN avidin assay which determined that 10.5 molecules of biotin per conjugated antibody from this hybridoina. Antibodies were purified using protein A affinity chromatography with a binding buffer of 0.5M NaCl in 0.1M Citrate/Phosphate buffer, pH=9.0 and an elution buffer of 0.1M citrate/phosphate, 0.15M NaC1, pH=3Ø The antibody eluted along a linear gradient with a pH range of elution from 6.4-3.9. See Figure 17. 21.8 mg of antibody were recovered.

[073] Referring to Figure 18 purity was determined to be 100 percent using size exclusion chromatography. Referrinp.. to Figure 19, the isoelectric point was determined to be around 6.5 using 20pil per well with a focusing conditions of 100v for 1 hour, 250v for 1 hour and 500v for 30 minutes.
Hybridoma 5

[074] Antibodies were generated using C57BL mice and hybridomas were created.
MBS
Accession: 15-0271RB3 for Cell Line: Bc1-2-61 Pep-KLH-BA-1.1-14A09-02C08-02F06 was conjugated with biotin and molar ratio quantified with HABN avidin assay which determined that 7.0 molecules of biotin per conjugated antibody from this hybridoma. Antibodies were purified using protein A affinity chromatography with a binding buffer of 0.5M NaC1 in 0.1M Citrate/Phosphate buffer, pH=9.0 and an elution buffer of 0.1M citrate/phosphate, 0.15M NaC1, pH=3Ø The antibody eluted along a linear gradient with a pH range of elution from 4.7-3.3. See Figure 20. 23.5 mg of antibody were recovered.

[075] Referring to Figure 21 purity was determined to be 100 percent using size exclusion chromatography. Referring to Figure 22, the isoelectric point was determined to be around 6.7 using 20 1 per well with a focusing conditions of 100v for 1 hour, 250v for 1 hour and 500v for 30 minutes.

Example 3: ELISA

[076] Research was conducted to identify monoclonal antibody pairs capable of specific detection of Bc1-2 in human urine sample matrix using a sandwich ELISA format at a clinically-relevant 1-20ng/mL sensitivity range.
Sandwich ELISA pre-work with Commercial Reagents:

[077] The commercial Bc1-2 reagents used for the initial assays are shown in Table 2.

[078] Table 2 Reagent Source mAb Bc1-2/100 Identified as an assay component in the Bender/eBioscience kit). Received two vials of 100 ug. One was biotinylated.
mAb Identified as an assay component in the 4D7 Bender/eBioscience kit, received additional 100 ug and performed biotinylation.
rBc1-2 R&D Systems product, Ala2-Asp211, with a C-terminal 10X His tag.
Normal For use in matrix testing. Received sample pool from human urine three donors; Lee BioSolutions.
SKOV-3 cell Cancer cell line, over-expressing human Bc1-2, for lysate evaluating detection of native, clinical samples.
Received one vial of 100 ug protein; Origene.
Bc1-2 HEK293T Origene; received two 20 ug vials, along with HEK293 overexpression negative control lysate.
lysate:
rBc1-2 MBS-produced recombinant Bc1-2, Metl-Asp211, with a C-terminal 10X His tag.

[079] A sandwich ELISA was developed reproducing the standard curve performance of the Bender Platinum Bc1-2 kit, using rBc1-2 proteins above from R&D Systems and an inhouse manufactured protein. Free and biotinylated forms of mAb Bc1-2/100 and mAb 4D7 were crossed in a sandwich ELISA with the R&D Systems protein.

[080] The most sensitive results were obtained with Bc1-2/100 capture antibody and 4D7 biotin conjugate. However, the sensitivity limited by the high negative sample optical density's (OD) observed with this antibody pairing.

[081] Side by side comparisons of the R&D Systems protein and the inhouse protein showed them to be functionally equivalent. OD values of pertinent concentrations of protein were directly comparable to the average ODs published in the Bender Platinum ELISA product insert.

[082] However, during semi-optimization of assay format, found lack of day to day reproducibility with the protein calibrators. Storage was at minus 80 C, and activity appeared to decline with freeze-thaw cycles.

[083] This led to investigations with multiple storage buffers and assay buffers. Selected a PBS-BSA system of blocking, sample diluent and conjugate diluent to minimize background while maximizing signal. Theorized that slow re- solubilization of the protein stock upon thawing is part of the consistency problem. Also believe that the problem is with the immune-stability of the protein, which may be alleviated with different antibody pairs.

[084] The final assay with these reagents included the SKOV-3 and HEK293 lysates. Each was run at a 1:5 dilution in sample diluent. The SKOV-3 sample had a blank-subtracted OD of 0.1, confounded by the negative HEK293 lysate at 0.09. The 10 ng/mL protein sample ran at 0.67, which puts it in line with the Platinum ELISA kit.
The Bc1-2-expressing lysate ran at 0.24 OD, but used an entire vial of the product for just the one assay.

[085] With the goal of measuring Bc1-2 in urine at concentrations less than 2 ng/mL in normal subjects to an average of only 4 ng/mL in cancer patients', a more sensitive ELISA is needed. Urine sample matrices are known to interfere with immunoassays2'3, often ameliorated by sample dilution. The more sensitive the assay, the higher the dilution factor can be while maintaining the target sensitivity range

[086] With this goal in mind, the generated anti-Bc1-2 hybridoma products will be screened for sandwich detection of rBc1-2 alongside the commercial antibody pairing.
Matched Pair Assay Characterization of Hybridoma Fusion Products:

[087] Materials:

[088] Hybridoma project BCL2-41 Pep-KLH-1.3 yielded 19 purified (MultiPure) fusion products; samples of each were conjugated to biotin. Four of the 19 yielded <0.2 mg antibody and were excluded from further testing.

[089] Hybridoma project BCL2-61 Pep-KLH-BA-1.1 yielded 20 purified (MultiPure) fusion products; samples of each were conjugated to biotin. Three of the 20 yielded <0.2 mg antibody and were excluded from further testing.

[090] Commercial mAb Bc1-2/100 capture antibody Commercial mAb 4D7-biotin conjugate

[091] rBc1-2 protein ¨ MBS lot 161071BP.1P

[092] Matched pair screenings were performed in two orientations: 15 Pep-41 captures x 17 Pep-61-biotin conjugates, and 17 Pep-61 captures x 15 Pep-41 biotin conjugates. All coatings were at 2 ug/mL and all biotins were at 1 ug/mL. Samples: Negative (sample diluent) and 25 ng/mL rBc1-2 in sample diluent. The commercial mAb pairing was repeated throughout the plates for comparison.

[093] Referring to Table 3 and Table 4, Initial heat maps showed clear superiority of 10Al2 as a capture with 14A09 and 18E10 as the tracer antibodies. Table 5 is a condensed heat map

[094]
Table 3 Bc1-2 Pep-41 Captures with Pep-61 Biotins 6' Absorbance Difference: 25 ng/mL Positive Well minus Negative well. OD <0.2 -a, Fusion Positive-Biotin Tracers W

o o 0 0 0 0 0 0 0 FA '' N '-' 1-' NJ 4, . N NJ W U.3 Do --.1 OD OD NJ A 4.
Do FA I--, Co ,D 0 O Avg.
Coated > co n -n CO > CO > = > > 2 > rn 0 . 1--, FA FA c, 0 0 0 , 0 0 0 0 F., 0 0 ,A Capture NJ NJ 0 0 ,-A W OD ln CO OD to J J
0 A CO .
OD
Fusion Positives ...:.........:.,:......4i:r.
01G11 003 EVAM.OE -0.01 0.11 0.02 0.00 0.01 0.05 -0.03 _AM. 0.01 -0 ... .02 ..:... ... . 6 ....: 010 0.3.
02807 ' 0.01 :::i.= ===== .-....9. -0.01 0.10 0.02 0.00 0.01 0.05 -0.01 iii 2.0,Ei 0.02 -0.01 mitigni::iiiiiginiff mic 0.16 0.4 ............. ? :::,,: =:::.:::.
02D04 0.02 : ::',;':0'2,..,:. ,:r.,,:xo.''''::: 0.00 0.05 0.01 0.00 0.00 0.02 -0.01 0.16 0.01 0.00 0.13 0.13 0.07 0.02 0.1 . = = = = `:i'?X::
I
03F04 0.01 : A.i., A.*,,1:. 0.00 0.09 0.01 0.01 0.00 0.04 0.00 ;:.? 0.01 -0.01 0.85 0.94 0,53 0.11 0.3 06E06 . 0.00 : 016 .::t..i:: 0.00 0.04 0.02 0.00 0.00 0.03 0.00 ,.*:i't 0.01 0.00 0.35 all 009 0.02 0.1 .......,,:::::::
P
06F06 0.01 :Wi:t:' v.$:.L aoo 0.04 0.01 0.01 0.00 0.04 0.00 *i*i:0::::%i*i: 001 aoo (L.?.
.;..1...:5.1.9:. .9.,?.. 0.10 0.3 ........ .........
06H05 0.00 0.04 017 -0.13 0.02 0.01 0.00 0.00 0.01 0.00 mg.c .... ro.p. 9 7ØT...
................ 31 002 0.02 0.0 o w 06H08 -0.01 0.05 0.07 -0.01 0.01 0.01 -0.01 aoo 002 -am. :J....A .õ aol -0.02 144 1I c. :3,...; ....!?..1 0.2 i--µ
ul 10Al2 AU PiNiigninglik 0.00 *4:0 g 0.10 0.07 44,A
0.00 "13: 0.17 0.01 t1 14 1.4 I, iv Gil cn 15C07 0.03 . ;=-= =;:- .4i7 0.00 0.13 0.03 0.02 0.00 0.07 0.00 iiiil.,:.,iniiiiii...: 0.03 0.00 Iiii*.4.iimiii.i3:] .?.,..;-: 0.18 0.4 -::':'..." ' = *,:',: ,. : !*: : : : : .......' rO' , 0.02 m....,;.:7'.,.i....:: :.:=:.:*:*1*.i..:0*.õ:......::':::' 0.00 0.13 0.02 0.02 0.00 0.08 0.00 :i.a4is20g 0.02 0.01 Q9 1, AiOk 0.16 0.4 Iv ' o 17D07 0.01 õ. *0 ww 0.00 0.08 0.02 0.01 0.00 0.05 0.00 .:.:t......W..:...: 0.01 0.00 ;µ,=,;::...=:M.......
õ.9....i.g..... W4t 0.10 0.3 '7 ul 18A07 0Ø0 . 4a: 0.00 0.04 0.02 0.01 0.00 0.04 0.00 ;:fmi 0.01 0.00 *gi vg gogi 0.07 0.2 19C04 0.01 ::::::::::::.. .....,....:.: -0.01 0.04 0.02 0.00 0.00 0.04 -0.01 :::,;1....:L. 001 aoa n...
:.t.,. 0.10 0.2 .,:.'.,.($:::
....'*i 20H06 0.01 :...i., ,,,,,......Am,,... 0.00 0.05 0.02 0.00 0.00 0.06 0.00 ..M.A.:.iii 0.02 0.00 ii*ii*i.i'i.iI.:.S:.1`.#:.:.A.:.:::.:::.:::.:::.:::.:::.:::.:::::,.:Sõ.::.::.::
.:.: r;,.e......IA.:.:::.:. 0.18 0.3 No Ab Ctl. -0.01 i 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.0 100/ 4D7 Bt in4N :::::::::::a *.3%: :::::::::14::::::::
.............................
:i*:.*ia'..;g7..:i:i ::::::::::13::::::: 1.3 Avg Conj OD 0.02 0.62 0.86 -0.01 0.12 0.03 0.01 0.01 0.08 0.00 1.00 0.02 0.00 0.99 1.03 0.63 0.22 . .
.0 n ,-i cp t..) -a, 4,.
c., oe ,.,.,

[095] Table 4 BcI-2 Pep-61 Captures with Pep-41 Biotins ..
Absorbance Difference: 25 ng/mL Positive Well minus Negative well. OD <0.2 :: = === = === '. ------------ :::::::::::::::;;;;;;;;..f.:.:.:.:.::::::::::::::::::
::::::::::::.:.:.:.:.:.:::::..:::::::::.:.::::::::::::::::::
k..) 1-, Antibody-Biotin Tracers Avg. Capture . 8 8 8 A A tal 1 sT1 A
OD
:
01Al2 0.01 : 0.12 0.07 -0.01 0.00 0.00 0.00 -0.01 0.01 0.00 : 0.03 0.06 0.07 0.00 0.01 0.0 02B12 Wigi 194 000 o.00 000 000 aoo 0.01 mt aoo a'.,i'i fiii i4i:;.g6!::4 aoo 0.04 0.5 =:Y:7i:i:::::========:=============:========.,:',::i:i:fff:
:==:=:=g ;;-= :=:..i:i:i:i:i:i:i:i:i:i:i:i:i:i:i i:i:i:i:i:i:i:i:i:i:i:i:i:i:i:
02C10 0.06 Ap... m..::. g 0.00 0.00 0.00 0.00 0.00 1118 000 a?,..m a1 114 OLO
0.03 0.3 03F10 0.01 0.06 0.03 0.00 0.00 0.00 0.00 -0.01 0.01 0.00 0.01 0.05 0.05 0.00 0.00 0.0 03G01 0.00 0.05 0.04 0.00 0.00 0.00 0.00 -0.02 0.01 0.00 0.02 0.07 0.13 0.00 0.02 0.0 05A05 0.03 0..N MC 0.00 0.00 0.01 0.00 -0.01 0.08 0.00 0.09 ining iMEN OLO 0.03 0.1 07609 0.02 0.09 0.06 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.02 0.04 0.02 0.00 0.01 0.0 P
09A05 0.01 0.07 0.05 -0.01 0.00 0.00 0.00 0.00 0.01 0.00 0.02 0.03 0.03 0.00 0.02 0.0 o L.
r 09 H 08 0.02 Ai:Mii 0.14 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.02 0.07 0.06 0.00 0.01 0.0 o ol 12A09 0.05 õP..:::3 :6,1:1L.; 0.00 0.00 0.01 0.00 0.01 um. 000 0.10 M5.33.N azo 0.00 0.02 0.1 ....1 I, IV
7.,_.''''''.: ::i:K:K.,:v::::::::::::::::::::::::::::::::::.::=:::::::::::
...:::., . Mi :i:]:;:::::K:::::::K*K
14A09 g.ft iiiiiiiiigia&i:,i:,i:,i:,i:,i:,i:,i:,igai 0.00 0.00 0.01 0.01 0.01 gog. 0.01 ma...,.m2.....,:....,:magi 0.00 0.04 0.6 o Iv 14 H 07 0.02 0.14 0.10 0.00 0.00 0.01 0.00 0.00 0.01 0.00 0.01 0.04 0.02 0.00 0.01 0.0 r o1 15A07 0.01 0.02 0.01 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.01 0.01 0.01 -0.01 0.00 0.0 r o1 M 0.00 0.00 0.00 001 001 Mi aoo at'ii ::::)::::::.:SiEla4.Yi.1:i 0.00 0.04 0.7 ol _...: \ """"""======= """"
===============================
18 E 10 I.A., ,,,,:z.. \\.. .*
.: ::....:t.... ':?.: mis iiiiiiT.....7.:5iiiiiiiii iiiiiiiIi.:48i*i*:
19 D 04 iM:,:''.iiiMi1...i9U aoo 0.00 aoo aoo 001 (1- nn 0 00 0 03 0 6 :
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii] lak:
iiiiAiiniiiiiiiii iiiiiiii]a8i:i:i: = ' ' 20A08 0.08 1.30 0.,.:T 0.00 0.00 0.00 0.00 0.01 0.19 ' 0.01 iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiai 0.00 0.04 0.3 20G11 0.06 ..#..et.: t.:.'..,.... 0.00 0.00 0.00 0.01 0.00 0.06 0.00 0.07 ....il: '31 c'....?.&. 0.00 0.02 0.1 No Ab Ctl. 0.00 0.01 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.0 100/ 4D-Bt :i:i:i:i:IA&:i:i:i:ii iiiiM 1.5 Avg. Conj OD 0.10 0.92 0.70 0.00 0.00 0.00 0.00 0.00 0.14 0.00 0.13 0.61 0.54 0.00 0.02 .0 n ,-i cp ,...) ,.., ---,-7.5 cT
Cie tin)

[096] Table 5 Absorbance Difference: 25 ng/mL Positive Well minus Negative well.

BcI-2 Pep-41 BcI-2 Pep-61 n.) o Coated Antibody-Biotin Tracers Coated Antibody-Biotin Tracers t,.) o 'a o o o o NJ NJ w 4.. 00 ks) 0 G')" iv ca iv ca o G) m o Fusion Fusion 1- 1- 0 8 . 0 8 N, , . . 0 4,.
Positives =Positives ............................*:*::Nom::::.::.::::
02612 1.94 1.60 :t:.g ,.;:.o.: 01G11 11 15 0.11 (..87 a Ã.4 0.67 0.33 0.10 .
02607 0 . ==== 0.9:1:.: 0.10 :i*,..:,... 1 10 1-22 11.1.:....i.....afF 016 02C10 0.79 C. 66 tat 114 !i!
- - ..
õ, õ __ ..............:::::::::::::::::::::::::::......................................
..:::::
03F04 0.3M
..:,..,..:õ.:,.: .. -, ,,; c: qn 0.E5,...:, 0.11 I
*!...-:i?X: :: 0.09 u "24 t.....c, ....
14/AuJ .:-...i...i.......2-..:91-......................................-2-.49:!:!:::::.....i:-. -:-.........-:-... -.....-:-.... -:-:
____________________________________________________________________________ =.i....:...Ogg.g.:::::::-:' ''''': .:;;:;44.: :..,.---:i4.-,;;;i:
06F06 .-'.:Ift M;==1:.' 0.04 .;.:::::µ,0pi c.,..,...,...
1.00 0.52 0.10 I 18E10 ::::::1:16::::=21.44 ii,i.!w r,,..:.y..
- ........................::::, .;,.....,,..,......,,......,...........,..,..,..,..,..,..,.. 1 w 06H08 0.05 0.07 1 0.01 .... :,.'', '-' '''s :==*...r..."$:"$:"..i"......"....:"...:"...:"...:"...::tr..........."..ii"i"...
.!..........Ø.....8....?.....................Ø...:1.....1 19D04 ::::::iiiiiiI9i3U: - ,..,...:...: .......:
.. =:":'.?...:::::=..*========.::::::::::::::::=?..*?...:-.,i--..,iiiiiii.ii.,:mr--ifff 10Al2 iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii --iigriNn';:::aii...ii.ii.i=iii....i.iiiiiiiiii1R......i.õ1.:.:..i!....Ø..õ....
......õ......,r1.i.,õi:i:i 20A08 1.30 :.) =.--:' i= 1.23 . .
1.16 , gi.i.........i.........iiiiiiiiiit n 1 q ]*.........ii.iiiiiiiiiiigimiw.
0.62 0.18 P
15C07 '1'..1:5 piiii.?!..e.iii ---::::,..........M=ii=iiiiiiiiiiiii........::.ff............... . ..c 0 ,,,...=-=:1,.*=:,:,= .::::::::E05,::;:::::: n i z iiiapiiiiiiiiiiiiii:iiiiilMiiiiiiiiiiiiiiii:440.iiiiiiiiiii 0 E:,: 0.16 r .......:..4.. ==========:***********':'*':::: --- :.**-ii...iii...*::::-...iii...i...i..:-....iiiiiiiii...*-....i.:-...i.:-...?:-...:-...:-...:-...:-...:-...:-...:-...:-...:-...:-...:-...:-....?.......C..............?.?.?.?.?.?..:-.
16E07,::,..,::::............................i.:x:
, ::":-:::::............:.::::::::::::
..............................................
17D07 c_:=:*:' :;::::!.4,;,?.11.i::i ....
0.08 u al C...79 0.92 0.4 '_-':
0.10 1 ND
, = = = = = = = = = =
=============================.:=::::::ii*iiiiiiiiiii , _, ND
. 1 0.05 q.....-in,..46......iiiiiii.......in,...:-..gnniiI5?-i=-?-i..i..i 0.õ, 0.18 I
20E106 (}..* i).34 i.i.........."........"..............i.i.i.i.i.i.i.i."..?.?....................
........i*i*?.?.?.?...........................................................
i o i--i o u, 1.44 1.13 1-d n ,-i cp t..) =
'a 4,.
=
c, oe ,...,

[097] Note that negative sample ODs for the pertinent pairings were all 0.08 or lower.

[098] Referring to Figure 23, in a subsequent ELISA, each of the 16 candidate capture antibodies were tested in pairs with 4 different biotin conjugates. Samples ranged from 0 to 20 ng/mL rBc1-2, and included 2 ug/mL rBc1- XL. None of the pairs showed any cross-reactivity to the 2 ug/mL rBc1-XL sample. The capture and conjugate antibody concentrations were not changed from the initial screen.
The data below illustrates samples of the resulting standard curves.

[099] Table 6 summarizes characteristics of all of the fusion positives.

[100]

[101] Table 6 TM-Pure yield Capture Conjugate mg/mL IEF Estimated pl senstivity sensitivity Comments MultiPures eliminated due to low antibody yield:
01F03 0.13 n/a 08H01 0.11 n/a 12806 0.02 n/a 12C12 0.11 n/a 06Al2 0.07 n/a 11F06 0.12 n/a 14E08 0.1 n/a MultiPures eliminated due to poor sandwich performance:
06E06 0.75 7.6- 7.8 +1- -06H05 0.54 8.2 -/-F -19C04 0.16 7.9 + -01Al2 0.18 too faint 6.8-7? - -03F10 0.18 faint 8.2? - -05A05 1.32 6.8- 7 +1- -1+
07609 1.01 6.7 - 7.1 - -09A05 0.28 faint 6.7 - 7.1 - -09H08 0.51 6.8 - 7.6 -1+ +1-12A09 0.25 7.5 - 8.1 +/- -14H07 0.73 6.9 - 7.2 - -15A07 0.16 faint 6.6 - 7.1 - -Functional MultiPures for further investigation:
01G11 0.7 7.1 - 7.8 ++ +1-02607 1.3 6.8 - 7.1 ++ +++
02D04 0.5 8.1 + +++
03F04 0.2 7.9 + -06F06 0.6 7.9 - 8 ++ -06H08 0.4 8.2 ++ -10Al2 0.6 6.4- 6.6 +++ +1-15C07 0.3 7.9- 8 ++ -16E07 1.1 8.2 ++ +1-17D07 1.1 7.6 - 7.9 + ++ Sister to 18A07 18A07 0.8 7.6- 7.9 + ++ Sister to 17D07 - eliminate 20H06 1.1 6.9 - 7.1 ++ -02612 0.3 6.1- 6.7 & 6.8- 7 ++ +++ Eliminate -polyclonal 02C10 1.1 6.75 - 7 ++ +++
03G01 0.9 6.8- 7.2 - +
14A09 0.8 6.75 - 7.1 +++ +++
18E10 0.7 6.4 - 6.6 +++ +++
19D04 1.0 6.6- 6.8 & 7.5- 7.8 +++ +++ Eliminate -polyclonal 20A08 1.1 6.7 - 7.2 ++ +++
20G11 1.0 6.6 - 7.1 + ++

[102] Shading indicates possible sister clones by IEF profile.

[103] The pairings that exhibited good sensitivity were semi-optimized for coating conditions and conjugate concentrations. An assay format similar to that of the Bc1-2 Platinum ELISA Kit was used.

[104] These antibody pairs were tested for matrix effect by fortifying rBc1-2 protein into varied dilutions of normal human urine (Lee Biosolutions lot 991-03-P). Note that this urine sample did not exhibit detectable levels of Bc1-2 in any of the pairings.

[105] Table 7 below illustrates the relative sensitivity of these pairings (absorbance values for rBc1-2 calibrators) as well as the recovery of the rBc1-2 fortifications (at 4 or 5 ng/mL).

[106] Table 7 _____________________________________________________________ normal Hu urine; urine rBCI-2 (ng/mL) dilution:
1 2.5 5 10 20 30 40 1:2 1:5 1:8 CAPTURE CONJUGATE Absorbance 450 nm minus 650 nm % Recovery 10Al2 18E10 0.3 0.9 1.6 2.7 76% 96%
108%
10Al2 14A09 0.2 0.7 1.4 2.5 74% 94%
106%
10Al2 02C10 0.1 0.3 0.7 1.6 72% 92%
94%
18E10 17D07 0.08 0.2 0.6 1.4 64% 76%
88%
18E10 02607 0.08 0.2 0.5 1.3 72% 88%
100%
16E07 14A09 0.2 0.4 0.9 1.8 2.3 2.7 68%
95%
20A08 17D07 0.1 0.3 0.6 1.2 1.7 2.0 85%
85%
20A08 02607 0.1 0.3 0.6 1.1 1.5 1.9 63%
68%
14A09 17007 0.15 0.2 0.5 1.2 1.7 60% 78%
90%
20H06 14A09 0.1 0.2 0.5 1.1 1.5 1.8 72% 92% 110%
02C10 17D07 0.1 0.2 0.3 0.5 0.8 1.0 78%
85%

[107] Peptide 41 Ab is in bold. Peptide 61 Ab is in normal font.

[108] The top two pairings of 10Al2/18E10 and 10Al2/14A09 were standouts for sensitivity. There was a trend for better recovery of fortified sample in urine with captures from the Peptide 41 hybridoma project. However, recoveries in the less sensitive pairings are likely affected by the 4 -5 ng/mL sample running at very low absorbance values.
Example 4 Sequencing

[109] The antibodies created in the examples above were sequenced. Two cryovials containing approximately 2 X 106 cells for clone 10Al2 and 14A09 were sent to Lake Pharma for sequencing. Lake Pharma isolated RNA from each sample and cloned the Heavy Chain Variable region (Vii) and Light Chain Variable region (VL) by RACE

PCR followed by ligation into a suitable vector. Multiple isolates of each clone were sequenced for each VH and VL.

[110] The nucleotide sequences obtained from Lake Pharma for each clone was submitted to IgBlast to determine the Complementarity-determining regions ("CDR") and Framework Regions ("FR") regions as well as determine the Vh, Dh, and Jh heavy chain (HC) gene usage and the V1 and Jl light chain (LC) gene usage for each clone.

[111] Clone 10Al2

[112] Referring to Figure 24, the protein sequence of the heavy chain is:

[113] QVQLQQSGPQLVRPGASVKISCKASGYSFTSYWMEIWVKQRPGQGLEWIGMI
DPSDSETRLNQKFKDKATLTVDKSSSTAYMQLSRPTFEDSAVYYCERGDYYY
GSSYFAYWGQGTLVTVSA (SEQ ID NO 14)

[114] Wherein CDR1 is GYSFTSYW (SEQ ID NO 15 and CDR2 is IDPSDSET (SEQ ID
NO16 ) and CDR3 is ERGDYYYGSSYFAY (SEQ ID NO 17)

[115] The amino acid sequence is coded by the DNA sequence of SEQ ID NO 18:

[116] CAGGT GCAACT GCAGCAGT CT GGGCCTCAGCT GGTTAGGCCT GGGGCTTCAGT GAAGATAT C
CT G
CAAGGC T T CT GGT TAT T CAT T CACCAGCTACT GGAT GCACT GGGT GAAGCAGAGGCCT
GGACAAG
GT CT T GAGT GGATT GGCAT GAT T GAT CCTT CC GATAGT GAAACTAGGTTAAATCAGAAGTT CAAG

GACAAGGCCACATT GACT GTAGACAAAT CC T CCAGCACAGCC TACAT GCAACTCAGCAGACC GAC
AT TT GAGGAC T CT GC GGT CTAT TACT GT GAAAGAGGGGAT TAT TAC TAC GGTAGTAGC TACT
TT G
CT TAT T GGGGCCAGGGGACT CT GGTCACT GT CT C T GCA (SEQ ID NO 18)

[117] Referring to Figure 25, the protein sequence of the light chain is:

[118] QAVVTQESALTTSPGETITLTCRSSTGAVTTSNYATWVQEKPDHLFTGLMGG
TTYRAPGVPARF SGSLIGDKAALTITGAQTEDEAMYFCALWF SNHFWVFGGG
TKLTVL (SEQ ID NO 19)

[119] Wherein CDR1 is TGAVTTSNY (SEQ ID NO 20) and CDR2 is GTT (SEQ ID NO
21) and CDR3 is ALWFSNHFWV (SEQ ID NO 22)

[120] The amino acid sequence is coded by the DNA sequence of SEQ ID NO 23:

[121] CAGGCT GT T GT GACT CAGGAAT CT GCACT CACCACAT CACCT GGT GAAACAAT CACACT
CACT T GT CGC
T CAAGTACT GGGGCT GT TACAAC TAGTAAC TAT GCCACCT GGGT CCAAGAAAAAC CAGAT CAT T
TAT T C
ACT GGT CT GAT GGGT GGTACCACCTACCGAGCT CCAGGT GT T CCT GCCAGAT T CT CAGGCT
CCCT GATT
GGAGACAAGGCT GCCCT CACCAT CACAGGGGCACAGACT GAGGAT GAGGCAAT GTAT T T CT GT GCT
CT T
T GGT T CAGCAACCAT T T CT GGGT GT T CGGT GGAGGAACCAAACT GACT GT CCTAG (SEQ ID
NO 23)

[122] By combining a sequence having a high homology with the above-described heavy chain amino acid sequence with a sequence having a high homology with the above-described light chain amino acid sequence, it is possible to select an antibody having improved specificity for BCL-2. The homology is generally a homology of 80% or more, preferably a homology of 90% or more, more preferably a homology of 95% or 96% or 97%, 98% or more, most preferably a homology of 99% or more.
Further, by combining an amino acid sequence including a substitution, deletion, or addition of one to several amino acid residues in the heavy chain or light chain amino acid sequence, it is also possible to select an antibody having a cytotoxic activity equivalent to that of each of the above-described antibodies. The number of amino acid residues to be substituted, deleted, or added is generally 10 or fewer, preferably 5 to 6 or fewer, more preferably 2 to 3 or fewer, most preferably 1.

[123] Clone 14A09

[124] Referring to Figure 26, the protein sequence of the heavy chain is:

[125] EVQLQQSGPELVNPGASVKMSCKASGYTFTDYYLDWVKQSHGESFEWIGRA
NPYNGVTNSNQKFKGKATLTVDMSSSTAFMELNSLTFEDSAVYYCARSSFDV
WGAGTTVTVSS (SEQ ID NO 24)

[126] Wherein CDR1 is GYTFTDYY (SEQ ID NO 25) and CDR2 is ANPYNGVT (SEQ
ID NO 26) and CDR3 is ARSSFDV (SEQ ID NO 27)

[127] The amino acid sequence is coded by the DNA sequence of SEQ ID NO 28:

[128] GAGGTCCAGCTGCAACAGTCTGGACCTGAGCTGGTGAACCCTGGGGCTTC
AGTGAAGATGTCCTGTAAGGCTTCTGGATACACATTCACTGACTACTACCT
GGACTGGGTGAAGCAGAGCCATGGAGAAAGCTTTGAGTGGATTGGACGT
GCCAATCCTTACAATGGTGTTACTAACTCCAACCAGAAGTTCAAGGGCAA
GGCCACATTGACTGTTGACATGTCCTCCAGCACAGCCTTCATGGAGCTCA
ACAGCCTGACATTTGAGGACTCTGCGGTCTATTATTGTGCAAGATCAAGCT
TCGATGTCTGGGGCGCAGGGACCACGGTCACCGTCTCCTCA (SEQ ID NO
28)

[129] Referring to Figure 27, the protein sequence of the light chain is:

[130] DIVITQDELSHPVTSGESVSISCRSSKSLLYKDGKTYLNWFLQRPGQSPQLLIY
LVSTRASGVSDRFSGSGSGTDFTLEISRVKAEDVGVYYCQQPVEYPFTFGSGT
KLEIK (SEQ ID NO 29)

[131] Wherein CDR1 is KSLLYKDGKTY (SEQ ID NO 30) and CDR2 is LVS (SEQ ID
NO 31) and CDR3 is QQPVEYPFT (SEQ ID NO 32)

[132] The amino acid sequence is coded by the DNA sequence of SEQ ID NO 33:

[133] GATATTGTGATAACCCAGGATGAACTCTCCCATCCTGTCACTTCTGGAGAATCAGTTTCCATCTCCTGC
AGGTCTAGTAAGAGTCTCCTATATAAGGATGGGAAGACATACTTGAATTGGTTTCTGCAGAGACCAGGA
CAATCTCCTCAGCTCCTGATCTATTTGGTGTCCACCCGTGCATCAGGAGTCTCAGACCGGTTTAGTGGC
AGT GGGT CAGGAACAGATTT CACCCT GGAAAT CAGTAGAGT GAAGGCT GAGGAT GT GGGT GT
GTATTAC
T GT CAACAACCT GTAGAGTAT CCATT CACGTT CGGCT CGGGGACAAAGTT GGAAATAAAA (SEQ ID
NO 33)

[134] By combining a sequence having a high homology with the above-described heavy chain amino acid sequence with a sequence having a high homology with the above-described light chain amino acid sequence, it is possible to select an antibody having improved specificity for BCL-2. The homology is generally a homology of 80% or more, preferably a homology of 90% or more, more preferably a homology of 95%
or 96% or 97%, 98% or more, most preferably a homology of 99% or more. Further, by combining an amino acid sequence including a substitution, deletion, or addition of one to several amino acid residues in the heavy chain or light chain amino acid sequence, it is also possible to select an antibody having a cytotoxic activity equivalent to that of each of the above-described antibodies. The number of amino acid residues to be substituted, deleted, or added is generally 10 or fewer, preferably 5 to 6 or fewer, more preferably 2 to 3 or fewer, most preferably 1.
Example 5: Lateral flow Assay

[135] The antibodies described in Example 2 were tested for use in a lateral flow assay.

[136] For the capture, each of the 5 clones was spotted at 0.5mg/mL on 4mm wide strips using moderate flow nitrocellulose membrane, (10 strips per clone so that negative vs.
+100ng/mL positive sample can be analyzed for each of the 5 clones), with a basic striping buffer, & a control spot (rPA). The sample pads and nitrocellulose were untreated.

[137] For the detector: each of the 5 clones were conjugated to 40nm gold under a standard conjugation protocol: middle pH, with medium-strong loading of the antibody onto the gold, a standard gold blocker, and then combined the gold conjugates 1:1 with a basic conjugate diluent containing sugar, buffer, protein & surfactant. We spot dried the gold + CD mixture onto each test strip, with each of the 5 conjugate + CD
mixtures 2 at a time for each of the strip sets from above (5 conjugates x2 strips each = 10 strips, for each of the 5 clone sets = 50 strips).

[138] We used a simple "synthetic" running buffer and for positive sample spiked @
10Ong/mL BCL-2.
A= 10Al2 B = 14A09 C = 18E10 D = 02C10 E= 17D07

[139] We looked for the best signal-noise (s/n) between negative vs.
positive signals, with lowest false positive possible. Zero false positives was not a requirement.

[140] Figure 28 shows Set "A" (A=Capture). The results were recorded at 20 mins and the best results are boxed in Figure 28. The best detector from Set-A = B.
C and D looked ok, but C/D/E conjugates crashed out of solution, leaving only B-conjugate Detector as a viable pair w/ A-Capture)

[141] Referring to Figure 29 set B, there was no Best Detector from Set-B.
Referring to Figure 30 Set C, the best Detector from Set C was A (boxed). Referring to Figures 31 and 32 sets D and E were not as good as A for detector. This may be because the C/D/E gold conjugates all crashed out of solution over time showing the difficulty of this assay. Also, E did not release from the pad well. The best Detector from Set-D =
A. There was no best detector from set E. The E detector showed the strongest overall signals, however E did not show any specificity for the target vs.
sample without target, hence E was not a good Capture.

[142] Referring to Figures 33-35, for each of the 3 "best" pairings noted above, we striped the 3 best Capture antibodies from A/C/D, at 0.5mg/mL with std.
striping buffer, goat anti-mouse control line, and for each of the 3 Capture antibodies, their best pair:

[143] A-capture with B-Detector (Figure 33)

[144] C-Capture with A-Detector (Figure 34)

[145] D-Capture with A-Detector (Figure 35): best

[146] In each picture we ran 3 sets. Within each set we ran 4 strips: 0, +1, +10, +100ng/mL BCL-2. Each of the 3 sets were different conjugate conditions of loading & pH comparison.

[147] After 4 more rounds of optimization of the conjugate & particularly the conjugate diluent, we selected the best condition in "dip strip" (standing upright) Lateral Flow Assay format (See Figure 36and then tried it in Cassette format (Figure 37), whereby we could also obtain digital readings with our reader designed for the cassettes. In Figure 37 we selected the best condition from top & then ran ratios of CD/CG. Dip strip vs. cassette requires further optimization.

[148] The best pairs were 1) 02C10 Capture ("D") with 10Al2 Detector ("A"), slightly better than set #2; 2) 18E10 Capture ("C") with 10Al2 Detector ("A"), definitively better than set #3; and 3) 10Al2 Capture ("A") with 14A09 Detector ("B").
Example 6: Retesting of Clones in EIA

[149] We performed additional testing of ETA testing of clones for BCL-2.
Well capture plates were coated in 200 ng/well in 1xPBS, lhr, blocked with 1% BSA, rinsed 4x (Phospahte buffered saline with tween) , stabilized with Stabilguard immunoassay stabilizer.

[150] We tested each biotinylated monoclonal at 1:1K dilution with 1:1K SA-HRP
(Streptavadin conjugated with horseradish peroxidase enzume) with and without 2ng/mL rBCL-2, 30 min incubation shaking at RT, 4x PBST wash. The plates were incubated with 3,3,5,5' 3,3',5,5'-Tetramethylbenzidine -Tetramethylbenzidine ("TMB") substrate for 7 min, stopped with an appropriate stop solution and read at 405nm. The results are shown in Table 8.

[151] Table 8 plate DO? Al2 Al2 EH) C10 A09 AV-Al2 Abs=>
_ + _ + _ + _ + _ + _ +
DO? 1.23 1.23 0.19 0.24 0.18 0.46 0.21 0.53 0.4 1.07 0.10 0.18 1:1K 1 8 5 2 5 4 2 1 9 5 Al2 0.05 0.04 0.01 0.03 0.02 0.18 0.02 0.13 0.05 0.11 0.03 0.12 1:1K 1 7 8 2 8 6 1 1 6 7 6 3 HO 1:1K 0.05 0.06 0.01 0.03 0.06 0.11 0.04 0.05 0.15 0.07 0.03 0.03 C10 0.04 0.04 0.01 0.03 0.05 0.18 0.04 0.02 0.13 0.03 0.00 0.00 1:1K 2 3 1 5 8 1 4 6 3 A09 0.19 0.58 0.05 0.20 0.14 0.19 0.08 0.05 0.13 0.09 0.01 0.00 1:1K 4 5 4 7 9 2 5 2 AV-Al2 0.03 0.02 0.01 0.05 0.12 0.12 0.00 0.03 0.02 0.08 0.02 0.00 1:1K 8 8 7 1 5 8 9 5 2 8 3 no 0.03 0.03 0.01 0.01 0.04 0.08 0.01 0.01 0.01 0.00 0.04 0 secondar 8 3 4 7 3 1 3 4 no 0.03 0.01 0.01 0.07 0.04 0.00 0.04 0.00 0.01 0.00 0.02 0 secondar 2 6 1 4 2 2 1 3 5 6 2 (+)=2ng/mL; 30 min incubation, 1:1K detector + 1:1K SA-HRP; 4xPBST wash, Xtreme TMB 7' w/stop; read at 405nm (200ng/well capture in 1xPBS for lhr; BSA block, w/stabilcoat on Greiner plates)

[152] The signal to noise ratio is shown in Table 9 below.

[153] Table 9 Signal to Noise plate Abs=> D07 Al2 E10 C10 A09 AV-Al2 D07 1:1K 1.01 1.29 2.55 2.49 2.68 1.70 Al2 1:1K 0.92 1.78 6.64 6.24 2.09 3.42 E10 1:1K 1.25 2.29 1.87 1.16 0.52 1.10 Clo 1:1K 1.05 2.38 3.27 0.70 0.26 0.50 A09 1:1K 3.07 4.10 1.39 0.71 0.66 0.13 AV-Al2 1:1K 0.74 3.00 1.02 3.33 3.28 0.11 no secondary 0.87 1.21 1.86 0.91 0.30 0.00 no secondary 0.50 6.73 0.05 0.07 0.40 0.00

[154] The best pairs are shown in bold. The best pairs for LFS are the Al2 detector with Eli) or C10 capture. The secondary set was A09 detector and Al2 capture

[155] The best pairs for ETA are Al2 detector with Eli) or C10 capture. The secondary set was A09 detector and Al2 capture References 1 Anderson N, Bermudez Y, Badgwell D, Chen R, Nicosia S, Bast Jr. R, Kruk P.
Urinary levels of Cc1-2 are elevated in ovarian cancer patients. Gynecologic Oncology 112 (2009) 60-67.
2Chatziharalambous D, Lygirou V, Latosinska A, et al. Analytical Performance of ELISA
Assays in Urine: One More Bottleneck towards Biomarker Validation and Clinical Implementation. PLoS ONE 11(2):e0149471. Koi:10.137/journal.pone 0149471.
2016.
3Taylor T, Janech, M, Slate E, et. al. Overcoming the Effects of Matrix Interference in the Measurement of Urine Protein Analytes. Biomarker Insights 7 (2012) 1-8.

Claims (63)

We claim:

1. An isolated antibody that binds to a human Bc1-2 protein, wherein the antibody is produced by a hybridoma cell line generated from SEQ ID No. 2, SEQ ID No. 3 or SEQ
ID No 11.

2. An isolated antibody that binds to a human Bc1-2 protein wherein the heavy chain is selected from SEQ ID NO: 14 or SEQ ID NO 24 and the light chain is selected from SEQ ID NO 19 or SEQ ID NO 29.

3. The antibody of claim 2 wherein the heavy chain is SEQ ID NO 14 and the light chain is SEQ ID NO: 19.

4. An antibody having at least 95% homology to the antibody of claim 3.

5. The heavy chain of the antibody of claim 3 wherein CDR1 is SEQ ID NO 15 and is SEQ ID N016 and CDR3 is SEQ ID NO 17.

6. The light chain of the antibody of claim 3 wherein CDR1 is SEQ ID NO 20 and CDR2 is SEQ ID NO 21 and CDR3 is SEQ ID NO 22. \

7. The antibody of claim 2 wherein the heavy chain is SEQ ID NO 24 and the light chain is SEQ ID NO : 29.

8. An antibody having at least 95% homology to the antibody of claim 7.

9. The heavy chain of the antibody of claim 3 wherein CDR1 is SEQ ID NO 25 and is SEQ ID NO: 26 and CDR3 is SEQ ID NO 27.

10. The light chain of the antibody of claim 3 wherein CDR1 is SEQ ID NO 20) and CDR2 is SEQ ID NO 21 and CDR3 is SEQ ID NO 22.

11. An antigen-binding fragment of the antibody of claim 1 that binds to a native sequence Bc1-2 polypeptide.

12. An antigen-binding fragment of the antibody of claim 2 that binds to a BCL-2 protein and wherein said antibody or antigen-binding fragment thereof binds a neoplastic cell or antigen thereof

13. A method for detecting BCL-2 comprising the steps of: reacting a patient sample with a monoclonal antibody of claim 1; and detecting a level of BCL-2 protein in the sample, wherein the sample collected from the subject is at least one sample selected from the group consisting of a urine sample, a saliva sample, a blood sample, a serum sample, and a plasma sample.

14. The method according to claim 13, wherein the monoclonal antibody is labeled.

15. The method according to claim14, wherein the monoclonal antibody is labeled with one or more labels selected from the group consisting of a biotin label, a fluorescent label, an enzyme label, a coenzyme label, a chemiluminescent label, a colloidal particle, and a radioactive isotope label.

16. The antibody of claim 2 further comprising a label.

17. The antibody of claim 16, wherein the label is selected from the group consisting of a biotin label, a fluorescent label, an enzyme label, a coenzyme label, a colloidal particle, a chemiluminescent label, and a radioactive isotope label.

18. The antibody of claim 3 further comprising a label.

19. The antibody of claim 18, wherein the label is selected from the group consisting of a biotin label, a fluorescent label, an enzyme label, a coenzyme label, a colloidal particle, a chemiluminescent label, and a radioactive isotope label.

20. The antigen-binding fragment of claim 4 further comprising a label.

21. The antigen-binding fragment of claim 12, wherein the label is selected from the group consisting of a biotin label, a fluorescent label, an enzyme label, a coenzyme label, a colloidal particle, a chemiluminescent label, and a radioactive isotope label.

22. An isolated antibody to Bc1-2 having a chromatography peak from 24-27 min.

23. An isolated antibody to Bc1-2 having an isoelectric point from about 6.5 to about 7.

24. A cDNA derived from an antibody of claim 1.

25. An expression vector comprising the cDNA of claim 24.

26. Capture antibody 10Al2.

27. A hybridoma producing capture antibody 10Al2

28. Antibody 18E10

29. A hybridoma producing capture antibody 18E10.

30. Antibody 14A09

31. A hybridoma producing capture antibody 14A09.

32. An immunoassay comprising capture antibody 10Al2 and labelled antibody 14A09.

33. The assay of claim 32 wherein the assay is selected from an ELISA or a lateral flow assay.

34. A method of detecting cancer in a patient comprising detecting BCL-2 in the urine or saliva of a patient using an immunoassay comprising capture antibody 10Al2 and labelled antibody 14A09 wherein detection of BCL-2 in concentrations above 2ng/m1 is indicative of cancer.

35. The assay of claim 34 wherein the assay is selected from an ELISA or a lateral flow assay.

36. An immunoassay comprising capture antibody 10Al2 and labelled antibody 18E10.

37. The assay of claim 36 wherein the assay is selected from an ELISA or a lateral flow assay.

38. A method of detecting cancer in a patient comprising detecting BCL-2 in the urine or saliva of a patient using an immunoassay comprising capture antibody 10Al2 and labelled antibody 18E10wherein detection of BCL-2 in concentrations above 2ng/m1 is indicative of cancer.

39. The assay of claim 38 wherein the assay is selected from an ELISA or a lateral flow assay.

40. An antibody to Bc1-2 wherein the light chain is SEQ ID NO 14 and the heavy chain is SEQ ID NO 14.

41. An antibody to BCL-2 wherein the complementarity determining regions of the light chain comprise SEQ ID NOS 15, 15 and 17and the complementarity determining regions of the light chain comprise SEQ ID NOS 20, 21 and 22.

42. An antibody to Bc1-2 having at least 90% homology to the antibody of claim 31.

43. An antibody to Bc1-2 having at least 95% homology to the antibody of claim 31.

44. An antibody to Bc1-2 having at least 96% homology to the antibody of claim 31.

45. An antibody to Bc1-2 having at least 97% homology to the antibody of claim 31.

46. An antibody to Bc1-2 having at least 98% homology to the antibody of claim 31.

47. An antibody to Bc1-2 having at least 99% homology to the antibody of claim 31.

48. An antibody to Bc1-2 wherein the light chain is SEQ ID NO 24 and the heavy chain is

49. An antibody to BCL-2 wherein the complementarity determining regions of the light chain comprise SEQ ID NOS 25, 26 and 27 and the complementarity determining regions of the light chain comprise SEQ ID NOS 30, 31 and 32.

50. An antibody to Bc1-2 having at least 90% homology to the antibody of claim 36.

51. An antibody to Bc1-2 having at least 95% homology to the antibody of claim 36.

52. An antibody to Bc1-2 having at least 96% homology to the antibody of claim 36.

53. An antibody to Bc1-2 having at least 97% homology to the antibody of claim 36.

54. An antibody to Bc1-2 having at least 98% homology to the antibody of claim 36.

55. An antibody to Bc1-2 having at least 99% homology to the antibody of claim 36.

56. A DNA sequence encoding the amino acid sequence of the antibody of claim 36.

57. A DNA sequence encoding the amino acid sequence of the antibody of claim 36.

58. A DNA sequence encoding the amino acid sequence of the antibody of claim 36.

59. A DNA sequence encoding the amino acid sequence of the antibody of claim 36.

60. An ELISA comprising the antibody of claim 29 and the antibody of claim 36.

61. A cDNA encoding the protein of SEQ ID NO 14, SEQ ID NO 19, SEQ ID NO 24 or SEQ
ID NO 29.

62. The cDNA of claim 57 wherein the cDNA is selected from SEQ ID NO 18, SEQ
ID NO
23, SEQ ID NO 28 or SEQ ID NO 33.

63. An RNA encoding the protein of SEQ ID NO 14, SEQ ID NO 19, SEQ ID NO 24 or SEQ
ID NO 29.