Patent Application
20230184787
The present invention relates to immunoassay methods for detecting and, preferably, quantifying human neutrophil elastase (HNE) generated fragments of calprotectin in a biofluid sample, and to the use of such methods for detecting, monitoring and/or determining the status or severity of a disease characterized by or exhibiting inflammation, such as but not limited to an inflammatory driven disease, in a patient. The present invention also relates to monoclonal antibodies and assay kits for use in such methods.
Calprotectin is expressed intracellularly, especially in neutrophil granulocytes, and comprises around 60% of neutrophil granulocytes total cytosolic matter (1). Calprotectin is a ligand for TLR receptors and is relatively protease resistant (2). Neutrophil granulocytes are specialized hematopoietic cells from the myeloid cell lineage and are a sub-group of cells from the innate immune system. Neutrophil granulocytes serve as a first in line of defense against pathogen and bacteria invasion, and are thus also highly expressed in inflamed tissue (3-5).
Calprotectin can be measured in the faeces (faecal-calprotectin) of patients with inflammatory bowel disease (IBD) (1), where faecal-calprotectin has proven to be a robust sandwich-ELISA biomarker for distinguishing IBD patients from patients with irritable bowel syndrome (6-8). As serum/plasma samples are much easier to handle than faecal samples, and as faecal consistency has also proven to affect faecal-calprotectin levels with high day to day and even stool to stool variation, many of the faecal-calprotectin assays have also been tested to see whether they could also be applied to serum/plasma samples. However, calprotectin has a very short half-life in plasma (5 hours) (9), and the current available data in regards to serum/plasma calprotectin and its utility as an applicable biomarker for IBD is controversial (10-15).
Activation of neutrophil granulocytes results in the production of neutrophil extracellular traps (NETs), where the cells secrete all their nuclei and cytosolic matter in an attempt to trap and impair e.g. invading bacteria (16). Calprotectin and human neutrophil elastase (HNE) will be secreted into the inflamed tissue, as a result of NET formation (17). Consequently, the tissue and extracellular matrix (ECM) and other secreted proteins will be degraded by HNE, which will result in the generation of neo-epitope containing protein fragments (18-19). In addition, HNE has also proven be related to tissue inflammation in IBD20. Neo-epitope containing protein fragments of collagen degradation and formation have been demonstrated to be measured in the serum from IBD patients and pre-clinical models and are associated with clinical disease parameters (18, 21-25).
Inflammation induced release of calprotectin and HNE also occurs in other diseases. Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by extensive inflammation and remodeling of the extracellular matrix (ECM) and this potentially leads to a severe decline in lung function over time (34,35). Neutrophils are highly abundant in a COPD-affected lung and cause persistent tissue damage (36). IPF patients experience similar persistent injury through fibrotic changes, where an increase of HNE release has been seen in bronchoalveolar lavage fluid for IPF patients (37). Neutrophils are cellular responders to inflammation and able to release both the protease NE and the protein calprotectin (38).
Inflammation also predisposes to the development of cancer and promotes all stages of tumorigenesis. Cancer cells, as well as surrounding stromal and inflammatory cells, engage in well-orchestrated reciprocal interactions to form an inflammatory tumor microenvironment (TME) (39). Immune checkpoint inhibitors, such as but not limited to anti-PD-1 therapies, are a class of drug used to treat cancers such as metastatic melanoma. However, peripheral biomarkers associated with response and resistance to anti-PD-1 therapies and other such immune checkpoint inhibitors in metastatic melanoma patients represent an unmet medical need. High neutrophil activity is also associated with immune checkpoint inhibitor failure, partially due to release of NETs which have been shown to protect tumor cells against cytotoxic attacks. As described above, HNE and calprotectin are the major NETs constituents.
The present inventors theorized that neo-epitope containing fragments of calprotectin generated by HNE could be a measure of active local tissue inflammation and active leucocytes including neutrophils, rather than systemic inflammation or circulating leucocytes. Furthermore, the present inventors have now developed a robust and reliable immunoassay for detecting and quantifying HNE-generated neo-epitope containing fragments of calprotectin in biofluids such as serum and plasma, and have demonstrated the use of said immunoassay in evaluating inflammation and disease activity in diseases such as IBD, COPD, IPF, metastatic melanoma, SCLC NSCLC, rheumatoid arthritis, ankylosing spondylitis, psoriasis, psoriasis arthritis and osteoarthritis.
Accordingly, in a first aspect the present invention relates to an immunoassay method for detecting an HNE-generated fragment of calprotectin, said method comprising contacting a human biofluid sample with a monoclonal antibody that specifically recognises and binds to an HNE-generated neo-epitope consisting of an N-terminus or C-terminus sequence of the HNE-generated fragment of calprotectin, and detecting binding between the monoclonal antibody and peptides in the sample.
Preferably, the detection is quantitative, and the method further comprises determining the amount of binding between said monoclonal antibody and peptides in the sample.
In preferred embodiments, the method is an immunoassay method for detecting and/or monitoring the progress of and/or determining the status or severity of a disease in a patient, wherein the disease is a disease characterized by or exhibiting inflammation, the method comprising contacting a biofluid sample obtained from said patient with the monoclonal antibody, detecting and determining the amount of binding between the monoclonal antibody and peptides in the sample, and correlating said amount of binding with values associated with normal healthy subjects and/or with values associated with a known status or severity of the disease and/or with values obtained from said patient at a previous time point and/or with a predetermined cut-off value.
The disease may be an inflammatory driven disease, such as for example inflammatory bowel disease (IBD), rheumatoid arthritis, psoriasis, psoriasis arthritis, ankylosing spondylitis, osteoarthritis, Sjögrens syndrome, or lupus.
In a preferred embodiment, the disease is inflammatory bowel disease (IBD). In particular, the immunoassay method may be a method for detecting and/or monitoring the progress of and/or determining the status or severity of types of inflammatory bowel disease (IBD) such as ulcerative colitis (UC) and/or Crohn's disease (CD).
In another preferred embodiment, the disease is rheumatoid arthritis, ankylosing spondylitis, psoriasis, psoriasis arthritis or osteoarthritis.
In other preferred embodiments, the disease may be chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF) or asthma.
In yet other embodiments the disease may be a cancer. The cancer may for example be a breast, prostate, lung, gastric, colorectal, pancreatic, melanoma, ovarian, kidney, head & neck, bladder cancer. The cancer may for example be a metastatic cancer. In particular embodiments, the cancer may for example be metastatic melanoma, small cell lung cancer (SCLC) or non-small cell lung cancer (NSCLC).
Where the method is a method for determining the status or severity of a disease, the method may for example be for assessing whether the disease is active or in remission; or for assessing a likely period of patient survival or progression-free survival; or for assessing a likely response to a medical intervention, such as a likely period of patient survival or progression-free survival with treatment with one or more drugs (such as one or more chemotherapeutic agents (i.e. cytotoxic agents) and/or immune checkpoint inhibitors).
The monoclonal antibody may specifically recognise and bind to an HNE-generated neo-epitope consisting of an N-terminus or C-terminus sequence of any HNE-generated fragment of calprotectin, such as any of the peptides listed in Table 2, infra. However, in certain preferred embodiments, the monoclonal antibody specifically recognises and binds to an N-terminus or C-terminus sequence of a peptide selected from one of the following HNE-generated fragments of calprotectin:
In a particular preferred embodiment, the monoclonal antibody specifically recognises and binds to an N-terminus or C-terminus sequence of the peptide
In certain preferred embodiments, the monoclonal antibody specifically recognises and binds to said N-terminus sequence of the HNE-generated fragment of calprotectin. Preferably, said monoclonal antibody does not specifically recognise or bind to an N-extended elongated version of said N-terminus amino acid sequence or an N-truncated shortened version of said N-terminus amino acid sequence. In this regard “N-extended elongated version of said N-terminus amino acid sequence” means one or more amino acids extending beyond the N-terminus of the sequence. Similarly, “N-truncated shortened version of said N-terminus amino acid sequence” means one or more amino acids removed from the N-terminus of the sequence. Thus, for example, where the monoclonal antibody specifically recognises and binds to an N-terminus sequence of the peptide KLGHPDTLNQGEFKELV (“NBH-222”) (SEQ ID NO: 1) an “N-extended elongated version” would be VKLGHPDTLNQ . . . (SEQ ID NO: 8), and an “N-truncated shortened version” would be LGHPDTLNQ . . . (SEQ ID NO: 9).
In certain other embodiments, the monoclonal antibody specifically recognises and binds to said C-terminus sequence of the HNE-generated fragment of calprotectin, wherein preferably said monoclonal antibody does not specifically recognise or bind to a C-extended elongated version of said C-terminus amino acid sequence or a C-truncated shortened version of said C-terminus amino acid sequence. In this regard “C-extended elongated version of said C-terminus amino acid sequence” means one or more amino acids extending beyond the C-terminus of the sequence. Similarly, “C-truncated shortened version of said C-terminus amino acid sequence” means one or more amino acids removed from the C-terminus of the sequence. Thus, for example, where the monoclonal antibody specifically recognises and binds to a C-terminus sequence of the peptide KLGHPDTLNQGEFKELV (“NBH-222”) (SEQ ID NO: 1) an “C-extended elongated version” would be . . . LNQGEFKELVR (SEQ ID NO: 10), and an “C-truncated shortened version” would be . . . LNQGEFKEL (SEQ ID NO: 11).
The monoclonal antibody is preferably a monoclonal antibody raised against a synthetic peptide comprising said N-terminus or C-terminus sequence. Thus, for example, where the monoclonal antibody specifically recognises and binds to an N-terminus sequence of the peptide KLGHPDTLNQGEFKELV (“NBH-222”) (SEQ ID NO: 1), the monoclonal antibody may be a monoclonal antibody raised against a synthetic peptide having the sequence KLGHPDTLNQ (SEQ ID NO: 12) such that the monoclonal antibody specifically recognises and binds to an N-terminus sequence of the peptide KLGHPDTLNQGEFKELV (SEQ ID NO: 1). Suitable exemplary protocols for raising a monoclonal antibody against a synthetic peptide are described in the Examples infra.
In certain exemplary embodiments, where the monoclonal antibody specifically recognises and binds to an N-terminus sequence of the peptide KLGHPDTLNQGEFKELV (“NBH-222”) (SEQ ID NO: 1), and preferably does not specifically recognise or bind to an N-extended elongated version of said N-terminus amino acid sequence or an N-truncated shortened version of said N-terminus amino acid sequence, the monoclonal antibody may preferably comprise one or more complementarity-determining regions (CDRs) selected from:
Preferably the monoclonal antibody comprises at least 2, 3, 4, 5 or 6 of the above listed CDR sequences.
Preferably the monoclonal antibody has a light chain variable region comprising the CDR sequences:
Preferably the monoclonal antibody has a light chain that comprises framework sequences between the CDRs, wherein said framework sequences are substantially identical or substantially similar to the framework sequences between the CDRs in the light chain sequence below (in which the CDRs are shown in bold and underlined, and the framework sequences are shown in italics)
KSSQSLLNSGNQKNYLA
WYQQKPGQPPKLLIY
GASTRES
GVPDRFTGSG
SGTDFTLTISSVQAEDLAVYYC
LNDHSYPYT
Preferably the monoclonal antibody has a heavy chain variable region comprising the CDR sequences:
Preferably the monoclonal antibody has a heavy chain that comprises framework sequences between the CDRs, wherein said framework sequences are substantially identical or substantially similar to the framework sequences between the CDRs in the heavy chain sequence below (in which the CDRs are shown in bold and underlined, and the framework sequences are shown in italics)
DHVIN
WVRQRTGQGLEWIGEIYPGSGSTYYNEKFKGKATLTADKSSNTA
YMQLSSLTSEDSAVYFCAW
FAY
Preferably, the monoclonal antibody comprises the light chain variable region sequence:
DIVMTQSPSSLSVSAGEKVTMSC
KSSQSLLNSGNQKNYLA
WYQQKPGQP
PKLLIY
GASTRES
GVPDRFTGSGSGTDFTLTISSVQAEDLAVYYC
LNDH
SYPYT
FGGGTKLEIK
and/or the heavy chain variable region sequence:
QVQLQQSGPELVKPGASVKMSCKASGYTFT
DHVIN
WVRQRTGQGLEWIG
EIYPGSGSTYYNEKFKG
KATLTADKSSNTAYMQLSSLTSEDSAVYFCAW
FAY
WGQGTLVTVSA
The biofluid sample may be any type of biofluid, such as for example blood, urine, synovial fluid, serum, bronchoalveolar lavage fluid (BALF), or plasma. In preferred embodiments, however, the biofluid sample is plasma or serum.
The immunoassay may be, but is not limited to, a competitive assay or a sandwich assay. Similarly, the immunoassay may be, but is not limited to, an enzyme immunoassay (EIA) or a radioimmunoassay. Preferably, the immunoassay is competitive assay. Preferably, the immunoassay is an enzyme-linked immunosorbent assay (ELISA), such as in particular a competitive ELISA.
In a second aspect, the present invention relates to a monoclonal antibody that specifically recognises and binds to an HNE-generated neo-epitope consisting of an N-terminus or C-terminus sequence of an HNE-generated fragment of calprotectin. The monoclonal antibody is suitable for use in an immunoassay according to the first aspect of the invention, and preferred and other optional embodiments of the monoclonal antibody according to the second aspect of the invention will be apparent from the discussion supra of the monoclonal antibodies for use the in the first aspect of the invention and preferred and other optional embodiments thereof.
In a third aspect, the present invention relates to an immunoassay kit comprising a monoclonal antibody according to the second aspect of the invention, and at least one of:
In a preferred embodiment, the immunoassay kit comprises the monoclonal antibody according to the second aspect of the invention, and one, two or all of:
Where, for example, where the monoclonal antibody binds to an N-terminus sequence of the peptide KLGHPDTLNQGEFKELV (“NBH-222”) (SEQ ID NO: 1) a suitable biotinylated peptide may be a peptide having the sequence KLGHPDTLNQ-L-Biotin (SEQ ID NO: 23), wherein L is an optional linker. Similarly, where the monoclonal antibody binds to an N-terminus sequence of the peptide KLGHPDTLNQGEFKELV (“NBH-222”) (SEQ ID NO: 1) a suitable calibrator peptide may be a peptide having the sequence KLGHPDTLNQ (SEQ ID NO: 12).
As used herein, the terms “peptide” and “polypeptide” are used synonymously.
As used herein the term “monoclonal antibody” refers to both whole antibodies and to fragments thereof that retain the binding specificity of the whole antibody, such as for example a Fab fragment, Fv fragment, or other such fragments known to those skilled in the art. Antibodies which retain the same binding specificity may contain the same complementarity-determining regions (CDR). The CDR of an antibody can be determined using methods known in the art such as that described by Kabat et al. (33).
Antibodies can be generated from B cell clones as described in the examples. The isotype of the antibody can be determined by ELISA specific for human IgM, IgG or IgA isotype, or human IgG1, IgG2, IgG3 or IgG4 subclasses. Other suitable methods can be used to identify the isotype.
The amino acid sequence of the antibodies generated can be determined using standard techniques. For example, RNA can be isolated from the cells, and used to generate cDNA by reverse transcription. The cDNA is then subjected to PCR using primers which amplify the heavy and light chains of the antibody. For example, primers specific for the leader sequence for all VH (variable heavy chain) sequences can be used together with primers that bind to a sequence located in the constant region of the isotype which has been previously determined. The light chain can be amplified using primers which bind to the 3′ end of the Kappa or Lambda chain together with primers which anneal to the V kappa or V lambda leader sequence. The full length heavy and light chains can be generated and sequenced.
As used herein, the framework amino acid sequences between the CDRs of an antibody are “substantially identical” or “substantially similar” to the framework amino acid sequences between the CDRs of another antibody if they have at least 70%, 80%, 90% or at least 95% similarity or identity. The similar or identical amino acids may be contiguous or non-contiguous. The framework sequences may contain one or more amino acid substitutions, insertions and/or deletions. Amino acid substitutions may be conservative, by which it is meant the substituted amino acid has similar chemical properties to the original amino acid. A skilled person would understand which amino acids share similar chemical properties. For example, the following groups of amino acids share similar chemical properties such as size, charge and polarity: Group 1 Ala, Ser, Thr, Pro, Gly; Group 2 Asp, Asn, Glu, Gln; Group 3 His, Arg, Lys; Group 4 Met, Leu, Ile, Val, Cys; Group 5 Phe Thy Trp.
A program such as the CLUSTAL program to can be used to compare amino acid sequences. This program compares amino acid sequences and finds the optimal alignment by inserting spaces in either sequence as appropriate. It is possible to calculate amino acid identity or similarity (identity plus conservation of amino acid type) for an optimal alignment. A program like BLASTx will align the longest stretch of similar sequences and assign a value to the fit. It is thus possible to obtain a comparison where several regions of similarity are found, each having a different score. Both types of analysis are contemplated in the present invention. Identity or similarity is preferably calculated over the entire length of the framework sequences.
As used herein, the term “N-terminus” refers to the extremity of a polypeptide, i.e. at the N-terminal end of the polypeptide, and is not to be construed as meaning in the general direction thereof. Likewise, the term “C-terminus” refers to the extremity of a polypeptide, i.e. at the C-terminal end of the polypeptide, and is not to be construed as meaning in the general direction thereof.
As used herein the term, the term “competitive immunoassay” refers to an immunoassay in which the target peptide present in a sample (if any) competes with known amount of target of peptide (which, for example, is bound to a fixed substrate or is labelled) for binding to an antibody, which is a technique known to those skilled in the art.
As used herein, the term “target peptide” refers to a peptide comprising or consisting of the HNE-generated neo-epitope, consisting of an N-terminus or C-terminus sequence of the HNE-generated fragment of calprotectin, that is specifically recognised and bound by the monoclonal antibody.
As used herein the term “sandwich immunoassay” refers to an immunoassay that uses at least two antibodies for the detection of an antigen in a sample, and is a technique known to the person skilled in the art.
As used herein the term “ELISA” (enzyme-linked immunosorbent assay) refers to an immunoassay in which the target peptide present in a sample (if any) is detected using antibodies linked to an enzyme, such as horseradish peroxidase or alkaline phosphatase. The activity of the enzyme is then assessed by incubation with a substrate generating a measurable product. The presence and/or amount of target peptide in a sample can thereby be detected and/or quantified. ELISA is a technique known to those skilled in the art.
As used herein the term “amount of binding” refers to the quantification of binding between monoclonal antibody and target peptide, which said quantification is determined by comparing the measured values of target peptide in the biofluid samples against a calibration curve, wherein the calibration curve is produced using standard samples of known concentration of the target peptide. In the specific assay disclosed infra which measures in biofluids target peptides having an HNE-generated neo-epitope consisting of an N-terminus sequence of the HNE-generated fragment of calprotectin: KLGHPDTLNQGEFKELV (“NBH-222”) (SEQ ID NO: 1), the calibration curve is produced using standard samples of known concentration of a calibration peptide having the N-terminus amino acid sequence KLGHPDTLNQ (SEQ. ID No. 12) (and which may in particular consist of the amino acid sequence KLGHPDTLNQ (SEQ ID NO: 12)). The values measured in the biofluid samples are compared to the calibration curve to determine the actual quantity of target peptide in the sample.
As used herein the “predetermined cut-off value” means an amount of binding that is determined statistically to be indicative of a high likelihood of a disease (i.e. a disease characterized by or exhibiting inflammation, such as for example an inflammatory driven disease) or a particular status or severity thereof (such as an active disease status or disease prognosis) in a patient, in that a measured value of a target peptide in a patient sample that is at or above the statistical cut-off value corresponds to at least a 70% probability, preferably at least an 75% probability, more preferably at least an 80% probability, more preferably at least an 85% probability, more preferably at least a 90% probability, and most preferably at least a 95% probability of the presence of said disease or said particular status or severity thereof.
As used herein the term “values associated with normal healthy subjects and/or values associated with known disease status or severity” means standardised quantities of the target peptide determined by the immunoassay method for subjects considered to be healthy, i.e. without a disease (i.e. a disease characterized by or exhibiting inflammation, such as for example an inflammatory driven disease), and/or standardised quantities of the target peptide determined by the immunoassay method for subjects known to have a disease (i.e. a disease characterized by or exhibiting inflammation, such as for example an inflammatory driven disease) of a known status or severity.
The presently disclosed embodiments described in the following examples are set forth to aid in the understanding of the disclosure, and should not be construed to limit in any way the scope of the disclosure as defined in the claims which follow thereafter. The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the described embodiments, and are not intended to limit the scope of the present disclosure nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.
In the following examples, the following materials and methods were employed.
Calprotectin fragments were generated in vitro by adding purified calprotectin, a heterodimer composed of the proteins S100A9 and S100A8, to an Eppendorf tube and adding human neutrophil elastase (HNE) in a protein:protease ratio of 100:1 (10 ug of calprotectin per 0.1 ug of HNE). The proteolytic reaction was inhibited after 24 hours by adding 5 mM EDTA stop buffer. Eppendorf tubes containing only protease buffer, or calprotectin without HNE, or HNE without calprotectin served as experimental controls.
100 μl of cleaved samples or controls were desalted with reverse-phase Vydac UltraMicro Spin C18 columns (Harvard Apparatus, cat #74-7206) according to the manufacturer's instructions. Non-targeted mass spectrometry analysis was performed on a quadrupole Orbitrap benchtop mass spectrometer, QExactive, (Thermo Scientific) equipped with an Easy nano-LC 1000 system (ThermoFisher Scientific). Separation was performed on 75 μm×25 cm, Acclaim Pepmap™ RSLC C18 capillary columns packed with 2 μm particles (ThermoFisher Scientific). A spray voltage of +2000 V was used with a heated ion transfer setting of 275° C. for desolvation. The on-line reversed-phase separation was performed using a flow rate of 300 nl/min and a linear binary gradient 85 min was used. The gradient started with 3% solvent B for 4 min, then going to 35% solvent B in 64 min, after which it goes to 45% solvent B in 5 min. Finally, the organic solvent concentration was increased up to 90% in 5 min and kept at 90% for 7 min. An MS scan (400-1200 m/z) was recorded in the Orbitrap mass analyzer set at a resolution of 70,000 at 200 m/z, 1×106 automatic gain control (AGC) target and 100 ms maximum ion injection time (44). The MS was followed by data-dependent collision-induced dissociation MS/MS scans at a resolution of 17,500 on the 15 most intense multiply charged ions at 2×104 intensity threshold, 2 m/z isolation width and dynamic exclusion enabled for 30 s.
Identification from discovery data was performed using the Homo sapiens proteome (UniProt proteome ID UP000005640, n20200 downloaded Dec. 6, 2015 with Proteome Discoverer 2.1 software (ThermoFisher Scientific). The processing workflow consisted of the following nodes: Spectrum Selector for spectra pre-processing (precursor mass range: 100-10000 Da; S/N Threshold: 1.5), Sequest-HT search engine (Protein Database: see above; Enzyme: No Enzyme; Max. missed cleavage sites: 2; Peptide length range 6-144 amino acids; Precursor mass tolerance: 10 ppm; Fragment mass tolerance: 0.02 Da; Dynamic modification: oxidation; Static modification: cysteine carbamidomethylation; and Percolator for peptide validation (FDR<0.01 based on peptide q-value). Peptide intensities were quantified using a proprietary algorithm developed in Proteome Discoverer 2.1 (ThermoFisher Scientific).
Briefly, generation of monoclonal antibodies targeting an HNE-generated neo-epitope consisting of an N-terminus or C-terminus sequence of an HNE-generated fragment of calprotectin (more specifically, targeting the N-terminus neo-epitope, also referred to herein as “CPa9-HNE”, of the HNE-generated fragment of calprotectin referred to as “NBH-222”) was carried out as follows.
Four to six-week old Balb/C mice were immunized subcutaneously with 200 μL emulsified antigen and 50 μg immunogenic peptide (KLGHPDTLNQ-GGC-Keyhole Limpet Hemocyanin (KLH) (SEQ ID NO: 24)) using Freund's incomplete adjuvant (Sigma-Aldrich). The mice were immunized at two-week intervals until stable serum titer levels were reached. The mouse with the highest serum titer was selected for monoclonal antibody production. The mouse was rested for one month and was then immunized intravenously with 50 μg immunogenic peptide in 100 μL 0.9% sodium chloride (NaCl) solution. After 3 days, splenocytes were isolated for cell fusion. In brief, splenocytes were fused with SP2/0 myeloma cells to produce hybridoma cells and then cloned in culture dishes using the semi-medium method. The clones were plated into 96-well microtiter plates, and limited dilution was used to secure monoclonal growth. The supernatants were screened for reactivity against the selection peptide (KLGHPDTLNQ (SEQ ID NO: 12)) and native material (serum and cleavage material) in an indirect competitive ELISA using streptavidin-coated plates (Roche, Hvidovre, Denmark, cat. 11940279). The clones with the best reactivity were purified using protein-G-columns according to the manufacturer's instructions (GE healthcare Life Sciences, Little Chalfont, Buckinghamshire, UK). These clones were tested for their reactivity toward the selection peptide and the elongated peptide, truncated peptide and non-sense peptide (see Table 1), and the clone showing the highest selectivity towards the selection peptide was chosen for monoclonal antibody production and assay development. Optimal incubation buffer, time, temperature, and optimal ratio between the biotinylated peptide and antibody were determined.
The monoclonal antibody chosen for production and assay development was also sequenced, and the CDRs and isotype determined. The sequence of the chains are as follows (CDRs underlined and in bold; N-terminus signal peptide and C-terminus Constant region in italics):
MEWRIFLFILSGTAGVHSQVQLQQSGPELVKPGASVKMSCKASGYTFTD
HVIN
WVRQRTGQGLEWIGEIYPGSGSTYYNEKFKGKATLTADKSSNTAY
QTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSS
SVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCICTVPEVS
SVFIFPPKPKDVLTITLTPKVTCVVVDISKDDPEVQFSWFVDDVEVHTA
QTQPREEQFNSTFRSVSELPIMHQDWLNGKEFKCRVNSAAFPAPIEKTI
SKTKGRPKAPQVYTIPPPKEQMAKDKVSLTCMITDFFPEDITVEWQWNG
QPAENYKNTQPIMDTDGSYFVYSKLNVQKSNWEAGNTFTCSVLHEGLHN
HHTEKSLSHSPGK
MESQTQVLISLLFWVSGACGDIVMTQSPSSLSVSAGEKVTMSCKSSQSL
LNSGNQKNYLA
WYQQKPGQPPKLLIYGASTRESGVPDRFTGSGSGTDFT
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKD
STYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
The levels of an HNE-generated neo-epitope consisting of an N-terminus or C-terminus sequence of an HNE-generated fragment of calprotectin (more specifically the levels of CPa9-HNE, i.e. the N-terminus neo-epitope of the HNE-generated fragment of calprotectin NBH-222) were assessed in samples by a solid phase competitive enzyme linked immunosorbent assay, which was carried out as follows.
96-well plates pre-coated with streptavidin (Roche Diagnostic's cat. No. 11940279, Hvidovre, Denmark) were coated with a biotinylated antigen (KLGHPDTLNQ-K-Biotin (SEQ ID NO: 27)) by incubation with the biotinylated antigen for 30 minutes at room temperature. Unbound biotinylated coater antigen was discarded, and the wells were washed with washing buffer (25 mM TRIZMA, 50 mM NaCl, 0.036% Bronidox L5, 0.1% Tween 20) using a standardized ELISA plate washing machine (BioTek® Instruments, Microplate washer, ELx405 Select CW, Winooski, USA). Samples were diluted in incubation buffer containing 1% bovine serum albumin (Sigma Aldrich, cat. No. a-7906, 98 purity) to maintain protein stability and for blocking. Samples and controls were added to the wells and incubated with the primary monoclonal antibody against the HNE-generated neo-epitope (CPa9-HNE), at 20° C. for 1 hour and agitated at 300 rpm. Unbound primary antibody and sample were discarded, and the wells were washed with washing buffer. Subsequently, HRP conjugated AffiniPure Rabbit anti-mouse IgG secondary antibodies (Jackson cat. No 315-035-045) was added to the wells and incubated for 1 hour at 20° C. Unbound secondary antibody was discarded by washing the wells in washing buffer. Chemiluminescence substrate (Roche Diagnostic's cat. No. 11582950001) was added to the well (100 μl/well), and the plates were incubated for 3 minutes at room temperature before reading the plates. Finally, an ELISA reader (VersaMAX; Molecular Devices, Wokingham Berkshire, UK) was used to quantify the relative light units (RLU) emitted from the plates at 440 nm and 650 nm. A standard curve was plotted using a 4-parametric mathematical fit model.
To test the robustness of the above assay, dilution recovery, peptide spiking in serum, analyte stability, freeze/thaw, antibody specificity (sanity test), interference (haemolysis, biotin, and lipids spiked in serum), inter/intra variance and biological relevance (cleavage material, serum and plasma) were tested.
Serums samples were tested from a patient cohort consisting of a total of 29 UC and 72 CD patients. Demographical data, disease history and therapy were obtained from electronic medical records and questionnaires. Anthropometric parameters were measured at the inclusion. Where available, patients' endoscopic disease activity was based on the simple endoscopic score for CD (SES-CD), and the Mayo endoscopic score for UC (MES). The MES score was used to add the information about disease extension26. Inflammatory activity was also defined as combination of clinical and biochemical disease activity using Crohn's Disease Activity Index (CDAI), partial Mayo score (pMayo) and C-Reactive Protein (CRP). Patient stratification based on endoscopic scores was done as follows: SES-CD (remission=0-2, mild=3-6, moderate=7-15, severe>15), MES (remission=0-2, mild=3-6, moderate=7-15, severe>15). Clinical and biochemical activity was defined as CDAI≥150 or CRP>5 for CD and pMayo>1 or CRP>5 for UC. Disease severity and extension were assessed by Montreal classification.
To achieve normal distribution, log-transformation of the data was applied prior to statistical analysis. Student t-test and one-way ANOVA for normally distributed data was applied for analysing statistical differences. If a normal distribution was not achieved by log transformation Mann-Whitney U-test and Kruskal Wallis was applied. False discovery rate method (FDR=5%) was used for multiple comparisons' correction. Target peptide levels are presented as non-log transformed data with mean and standard error of the mean (SEM).
For the purpose of assessing the diagnostic power of the target peptide, receiver operating characteristic (ROC) curves were calculated. A P-value of ≤0.05 was considered statistically significant. Statistical analysis was performed using Graphpad Prism 7.03 and MedCalc. Figures were made using GraphPad Prism version 7.03.
CPa9-HNE was measured in serum from COPD patients (n=68) and healthy controls (n=36), and IPF patients (n=16) and healthy controls (n=10).
CPa9-HNE was measured in pre-treatment serum from metastatic melanoma patients treated with anti-PD-1 therapy (pembrolizumab) (n=35). The patients were treated with pembrolizumab as the standard of care at Copenhagen University Hospital, Herlev, after informed consent and approval by the Ethics Committee for the Capital Region of Denmark in compliance with the Helsinki Declaration 1975. Serum samples were measured blinded. The association between CPa9-HNE levels and progression-free survival (PFS) and overall survival (OS) were assessed by Kaplan Meier analyses and Cox regression analyses, alone and after adjusting for PDL1 expression (≥1%), lactate dehydrogenase (LDH), BRAF mutational status, and C-reactive protein (CRP).
CPa9-HNE was measured in serum from patients with small cell lung cancer (SCLC), patients with non-small cell lung cancer (NSCLC), and healthy controls.
CPa9-HNE was measured in serum from patients with rheumatoid arthritis (n=15, age [range: 39-47]), psoriatic arthritis (n=11, age [range:31-64]), psoriasis (n=12, age [range: 27-52]), ankylosing spondylitis (n=11, age [range: 35-53]), young osteoarthritis (n=13, age<51 [range: 41-50]), old osteoarthritis (n=10, Age>50) and healthy controls (n=33). 41 of the patients were female.
The non-targeted mass spectrometry analysis and subsequent calprotectin fragment identification, applying UniProt proteome ID UP000005640, revealed that several neo-epitope containing calprotectin fragments were generated by HNE, from both the S100A9 and S100A8 proteins (Table 2, and
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The mass spectrometry data demonstrated that NBH-222 was only present in samples containing full length human calprotectin+human neutrophil elastase, but not in the control samples containing only full-length human calprotectin or human neutrophil elastase (
CPa9-HNE levels in serum from IBD patients were demonstrated to correlate to faecal calprotectin levels (i.e. levels of intact calprotectin in faeces) and neutrophil count in UC patients (
The serum levels of CPa9-HNE were measured in serum from UC, CD and healthy subjects. CPa9-HNE was demonstrated to be ˜4-fold higher in the serum of IBD patients compared healthy subjects (AUC: 0.92, P<0.0001) (
CPa9-HNE is Associated with Endoscopic Disease Activity in UC and CD
CPa9-HNE correlated well with endoscopic disease activity for CD (SES-CD: r=0.057, P<0.0001) and UC (MES: r=0.71, P=0.0003) (
CPa9-HNE is Associated with Clinical Disease Activity in UC
Dividing the UC patients into clinical remission and clinical active disease based on the partial mayo score, CPa9-HNE was significantly elevated in UC patients with clinical active disease compared to UC patients in remission (AUC: 0.88, P<0.0001) and healthy donors (AUC: 0.93, P<0.0001) (
CPa9-HNE was measured in serum samples for COPD patients and healthy controls.
CPa9-HNE was measured in serum samples for IPF patients (n=16) and healthy controls (n=10).
High CPa9-HNE is Associated with a Worse Prognosis in Metastatic Melanoma
The association between CPa9-HNE and survival outcomes in the metastatic melanoma patients was evaluated by Kaplan-Meier analysis. Using the 75th percentile cut point, it was found that patients with high CPa9-HNE levels (>75th percentile) had significantly worse PFS (p=0.011) and OS (p=0.0002) compared to patients with low CPa9-HNE levels (
CPa9-HNE was measured in serum from patients with small cell lung cancer (SCLC), patients with non-small cell lung cancer (NSCLC), and healthy controls. The Lung cancer patients experienced a statistically significant increase in CPa9-HNE serum levels, where both small cell lung cancer (SCLC) (p=0.0435, n=10, median=212.1 [IQR 164.0-407.1]) and non-small cell lung cancer (NSCLC) (p=0.0467, n=10, median=281.3 [IQR 186.8-385.8]) were examined (
The CPa9-HNE was measured in serum from patients with rheumatoid arthritis (n=15, age [range:39-47]), psoriatic arthritis (n=11, age [range:31-64]), psoriasis (n=12, age [range:27-52]), ankylosing spondylitis (n=11, age [range:35-53]), young osteoarthritis (n=13, age<51 [range:41-50]), old osteoarthritis (n=10, Age>50) and healthy controls (n=33). The CPa9-HNE biomarker was significantly elevated in all joint disease compared to healthy controls, with the greatest difference being observed for ankylosing spondylitis (p<0.001), psoriatic arthritis (p<0.001), young osteoarthritis (p<0.001), and rheumatoid arthritis (p<0.01) patients compared to healthy controls (
In this study the inventors have demonstrated that the CPa9-HNE assay is technically robust with biological and clinical relevance as a serum based assay for detecting, inter alia, IBD, COPD, IPF, SCLC, NSCLC, rheumatoid arthritis, ankylosing spondylitis, psoriasis, psoriasis arthritis and osteoarthritis, and assessing disease activity. Additionally, the inventors have demonstrated that the CPa9-HNE assay is of prognostic value in patients with metastatic melanoma.
As indicated in table 3 the CPa9-HNE containing calprotectin fragment (NBH-222) is stable at 4° C. for a minimum of 48 hours in serum, which also means that this neo-epitope containing fragment has a much longer half-life than intact calprotectin in serum and plasma, intact calprotectin having only a half-life of 5 hours in plasma (9) despite being proven to be stable in faeces for 7 days (1). This may explain the poor clinical applicability of the faecal calprotectin assays when applied to serum/plasma, which assays performance is similar to CRP (10-12). The high stability of the CPa9-HNE fragment in serum (minimum 48 hours at 4° celcius) may be explained by the fact that it is a degradation product/metabolite of calprotectin, making the fragment more resistant for further degradation. In addition, the CPa9-HNE assay is also more sensitive than the faecal calprotectin assay, since it measures nanograms/mL instead of micrograms/gram (27).
Calprotectin's ability to bind metal ions e.g. calcium and zinc ions makes it highly resistant towards to metalloproteinase (MMP) degradation since MMPs require Zinc ions for activation. HNE is a serine protease and does not require activation by metal ions and is thus able to degrade calprotectin and generate HNE derived neo-epitope containing calprotectin fragments (5, 28-30). Therefore, CPa9-HNE levels may be representative of local tissue inflammation, as CPa9-HNE containing fragments will only be generated by activated neutrophil granulocytes and other activated leukocytes, and only the presence of HNE. This, is in contrast to intact calprotectin which can be released randomly into the circulation and faeces by non-activated circulating leukocytes and to some extent by epithelial cells, which also express calprotectin (10,31,32).
CPa9-HNE was demonstrated to be highly abundant in serum of CD and UC patients, indicating high potential as surrogate biomarker aiding diagnosis of IBD. This is in concordance with faecal calprotectin as this biomarker can reliably distinguish between IBS and IBD patients (6-8). Furthermore, CPa9-HNE also correlated with faecal calprotectin, neutrophil granulocyte count and disease activity for CD and UC, indicating that CPa9-HNE can be used to monitor disease activity and may be surrogate biomarker for endoscopic assessment for CD and UC.
The CPa9-HNE assay also elucidated a significant difference between patients affected with pulmonary diseases COPD, and IPF as compared to healthy controls. The CPa9-HNE assay measures a specific cleavage site on calprotectin that is generated by neutrophil elastase. Therefore, these results indicate a higher activity of NE in these pulmonary diseases.
The CPa9-HNE assay was also demonstrated to be predictive of overall and progression free survival rates in patients with metastatic melanoma treated with treated with anti-PD-1 therapy, based on baseline (pre-treatment) concentrations of serum CPa9-HNE.
Finally, CPa9-HNE was also shown to be significantly elevated in the serum of lung cancer patients (both SCLC and NSCLC) as compared to healthy controls, and in the serum of rheumatoid arthritis, ankylosing spondylitis, psoriasis, psoriasis arthritis and osteoarthritis patients as compared to healthy controls.
The CPa9-HNE ELISA was proven to have high specificity towards the neo-epitope both in in vitro cleavage samples and in the human IBD serum samples as a novel serum biomarker for HNE mediated degradation of calprotectin. CPa9-HNE was highly associated with CD and UC patients and demonstrated high diagnostic accuracy to differentiate IBD patients from healthy donors. Furthermore, CPa9-HNE also correlated with endoscopic disease activity for CD and UC, SES-CD and MES respectively. CPa9-HNE also correlated with clinical disease activity scores for UC (partial Mayo score and the Trulove and Witts score). Therefore, the CPa9-HNE is a surrogate biomarker of disease activity for CD and UC, and performed at least as well as or slightly better than Faecal-CP. Therefore, CPa9-HNE is a novel clinically relevant biomarker for IBD diagnosis and monitoring of disease activity, as well as also other inflammatory driven diseases including, rheumatoid arthritis, psoriasis, psoriasis arthritis, ankylosing spondylitis, osteoarthritis, Sjögrens syndrome, and lupus. It may also be uses to predict or monitor treatment efficacy in e.g. TNF-alpha, vedolizumab and ustekinumab prospective studies.
Additionally, CPa9-HNE has been shown to be a clinically relevant biomarker in lung diseases such as COPD and IPF, metastatic diseases such as metastatic melanoma, and lung cancers such as SCLC and NSCLC.
In this specification, unless expressly otherwise indicated, the word ‘or’ is used in the sense of an operator that returns a true value when either or both of the stated conditions is met, as opposed to the operator ‘exclusive or’ which requires that only one of the conditions is met. The word ‘comprising’ as used herein means ‘including’ or ‘consisting of’. All prior teachings acknowledged herein are hereby incorporated by reference.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2007087.6 | May 2020 | GB | national |
| 2100902.2 | Jan 2021 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2021/062753 | 5/12/2021 | WO |
