# Patent

## Title
Identification method of glycoproteins using a specific lectin precipitation

## Abstract

The present invention relates to an analyzing method of measuring the changes of glycosylation in various glycoproteins which participate in tumorigenesis and metastasis.

## Background
CROSS-REFERENCE TO RELATED PATENT APPLICATIONS
This application is a continuation application under 35 U.S.C. §365(c) of International Application No. PCT/KR2007/006124, filed Nov. 30, 2007 designating the United States. The International Application No. PCT/KR2007/006124 was published in English as WO2009/048196 A1 on Apr. 16, 2009. This application further claims the benefit of the earlier filing date under 35 U.S.C. §365(b) of Korean Patent Application No. 10-2007-0100916 filed Oct. 8, 2007. This application incorporates herein by reference the International Application No. PCT/KR2007/006124 including the International Publication No. WO2009/048196 A1 and the Korean Patent Application No. 10-2007-0100916 in their entirety.


BACKGROUND
1. Field
The present invention relates to a detection method of glycoproteins that exhibit an alteration in glycosylation in the course of tumorigenesis and cancer metastasis. More specifically, the present invention relates to a mass spectrometry (MS)-based identification of N-linked glycoproteins that are modified during cancer development and progression.
2. Discussion of the Related Technology
Two-dimensional electrophoresis allowed to identify and characterize proteins with ease and in a high-throughput manner when connected to such highly sophisticated analyzers as MALDI-TOF (Matrix Assisted Laser Desorption/Ionization Time-of-Flight) mass spectrometry and amino acid sequencers, whose developments have facilitated the ‘post-genomics proteomics era’. However, the proteomics approaches have a limitation in that they present a fixed state of proteome rather than revealing a biological dynamism. In fact, signal transduction pathways in cells generally exhibits an dynamism in the expression level of proteins and post-translational modification (PTM).
Moreover, it is often difficult to monitor the proteins on the signal transduction pathway by displaying 2-D gels since the proteins exist sparsely in cells. Protein glycosylation allows to overcome these limitations and to observe cells on a dynamism-basis. Changes in proteins level that can not be discerned by simple staining are easily monitored when alterations in glycosylation are chased with a specific lectin.
Recently, this approach, termed ‘glycomics’, has emerged as a promising field that help overcome the limitations of the conventional proteomics. Glycomics is mainly based on pursuit of alterations in protein glycosylation, a major class of post-translational modification.
One of the biological disturbances is an aberrant glycosylation of proteins, which is induced by a signal of a certain oncogene and causes, in turn, a dysfunction of cell adhesion, cell-cell recognition and eventually tumorigenesis and cancer malignancy (Hakomori and Kannagi, 1983, J. Natl. Cancer Inst., 71:231-251; Feizi, 1985, Nature, 314:53-57). Matured mRNA is translated on an endoplasmic reticulum, where core glycan moiety of N-linked glycosylation is also generated. After that, the glycoproteins are translocated to Golgi body where supplementary glycans are attached by such glycosyltransferase as illustrated in FIG. 1. The glycosyltransferases are activated by a signal elicited by the specific oncogenes, such as ras, raf, ets, and so on. One of the glycosyltransferases that draw interests is FUT8, which catalyzes an addition of fucose to the core N-acetylglucosamine (GlcNAc) of N-glycan. Alpha-fetoprotein (AFP) and antitrypsin are widely known to exemplify the importance of a fucosylation in cancer malignancy (Miyoshi, E., Ko, J. H. et al., 1999, Biochim. Biophys. Acta 1473: 9-20). FUT8 (Fucosyl transferase 8) responsible for the fucosylation was purified and the cDNA was cloned by Taniguchi group and when FUT8-transfected Hep3B (Hep3B-FT) was injected into the spleen of athymic mice, tumor formation in the liver was dramatically suppressed in the transfectants compared to the parental cells (Miyoshi, E., Ko, J. H. et al., 1999, Cancer Research 59: 2237-2243). Lens culinaris agglutinin (LCA) bind the fucose attached to the innermost GlcNAc of N-glycan and also core N-glycan like Con A.
The aberrant glycosylation induced by N-acetylglucosaminyltransferase V (GnT-V) is a representative example of such protein modifications as are implicated in the tumor invasion and metastasis (Dennis et al., 1987, Science, 236:582-585). Following the attachment of core glycans on endoplasmic reticulum, the supplementary glycans are decorated in Golgi body primarily by 6 types of N-acetylglucosaminyltranferase (I-VI). Of these, GnT-V is known to be associated with metastatic potential of cancer cells by modifying the target glycoproteins and changing the properties of recognition and cell adhesion of cancer cells.
GnT-V was first noticed by the report of Dennis et al. (1987) that the β1,6 branches were remarkably represented as cancer tissues were growing or during metastasis (Dennis, et al., 1987, Science, 236: 582-585). A cell surface protein gp130 is one or major target proteins of GnT-V and shows high metastasis activity when β1,6 N-acetylglucosamine is added. GnT-V knockout mice were established in which GnT-V was deficient in their embryonic stem (ES) cells and to which polyomavirus middle T antigen (reffered “PyMT” hereinafter) viral oncogene was introduced in order to induce a cancer. Resultingly, the growth of cancer and metastasis induced by PyMT were remarkably inhibited in GnT-V knockout mice comparing with another normal mice group in which only PyMT was over-expressed (Granovsky et al., 2000, Nature Med., 6: 306-312), and the growth of β1,6 branch caused high metastasis especially in mice with breast cancer. As shown above, GnT-V relates to cancer metastasis and represents high matastasis activity in various tissues. GnT-V was purified in the human lung cancer cell and the mouse kidney, the cDNA was cloned, and the promoter and genomic structure was resolved (Gu et al., 1993, J Biochem, 113:614-619; Soreibah et al., 1993, J. Biol. Chem., 268:15381-15385; Kang et al., 1996, J. Biol. Chem., 271:26706-26712). The inventor of the present invention has reported that the transcription factor ets-1 is involved in the expression of GnT-V (Ko, et al., 1999, J. Biol. Chem., 274(33): 22941-22948). Limitations of the drug-based cancer treatment triggered a paradigm shift in the medical cancer researches toward early detection at a curable stage, and the aberrant glycoproteins are being tested for use as a cancer early-detection marker.
In accordance with this, the inventors of the present invention have reported a list of candidate proteins from cancer cells with high GnT-V overexpression that show an attachment of β1,6-GlcNAc by GnT-V using 2-dimensional electrophoresis and mass spectrometry (Kim et al., 2004, Proteomics, 4: 3353-3358; Kim et al., 2006, Proteomics, 6: 1187-1191). However, the previous gel-based resolution procedures innately have a high incidence of false-positive rates in the identification of sparse proteins. To overcome this, the inventors completed the present invention by enriching β1,6-GlcNAc-carrying glycoproteins using L-PHA lectin to identify them.
SUMMARY
One aspect of the invention provides a method of analyzing a sample to determine a level of a β1,6-N-acetylglucosamine-containing glycoprotein. The method comprises: providing a test agent comprising a first complex, wherein the first complex comprises a glycan bead and an phytohemagglutinin-L4 (L4-PHA) moiety connected to the glycan bead, wherein the L4-PHA moiety comprises a binding site specific to β1,6-N-acetylglucosamine; providing a sample comprising a β1,6-N-acetylglucosamine-containing glycoprotein; contacting the test agent with the sample to provide a test mixture, in which the β1,6-N-acetylglucosamine-containing glycoprotein binds with the first complex at the binding site, thereby forming a second complex in the mixture, wherein the second complex comprises the glycan bead, the L4-PHA moiety and the β1,6-N-acetylglucosamine-containing glycoprotein as a single entity; heating and applying a denaturing agent to the second complex to provide a denatured mixture, in which the β1,6-N-acetylglucosamine-containing glycoprotein may be disassociated from the L4-PHA moiety and the glycan bead; separating the glycan bead from the denatured mixture to provide the β1,6-N-acetylglucosamine-containing glycoprotein substantially free of the glycan bead; subsequently fragmentizing the β1,6-N-acetylglucosamine-containing glycoprotein into smaller fragments; and analyzing the fragments using a mass spectrometric procedure to determine a level of the β1,6-N-acetylglucosamine-containing glycoprotein in the sample.
The foregoing method may further comprise: collecting, from the test mixture, compounds and complexes that comprise a glycan bead while substantially excluding other compounds and complexes that do not contain a glycan bead, wherein the collected compounds and complexes comprise the second complex. The first complex may further comprise a bridge interconnecting the glycan bead and the L4-PHA moiety, wherein the bridge may comprise a ligand receptor and a ligand engaged with the ligand receptor, wherein the ligand may be attached to one of the L4-PHA moiety and the glycan bead, wherein the ligand receptor may be attached to the other of the L4-PHA moiety and the glycan bead. Heating and applying a denaturing agent may cause to disengage the ligand from the ligand receptor, thereby further disassociating the L4-PHA moiety from the glycan bead, whereby the denatured mixture may comprise the β1,6-N-acetylglucosamine-containing glycoprotein, the L4-PHA moiety and the glycan bead as separate entities. Separating may comprise running an electrophoresis in a gel medium, thereby separating the glycan bead from the β1,6-N-acetylglucosamine-containing glycoprotein and the L4-PHA moiety in the denatured mixture. Fragmentizing may comprise contacting an enzymatic agent with the β1,6-N-acetylglucosamine-containing glycoprotein and the L4-PHA moiety.
In the foregoing method, the first complex may further comprise a bridge interconnecting the glycan bead and the L4-PHA moiety, wherein the bridge may comprise a biotin and an avidin engaged with the biotin, wherein the biotin may be attached to one of the L4-PHA moiety and the glycan bead, wherein the avidin may be attached to the other of the L4-PHA moiety and the glycan bead. Separating may comprise running an electrophoresis in a gel medium, thereby separating the glycan bead from the β1,6-N-acetylglucosamine-containing glycoprotein. Fragmentizing may comprise contacting an enzymatic agent with the β1,6-N-acetylglucosamine-containing glycoprotein. The enzymatic agent may be applied to the gel medium containing the β1,6-N-acetylglucosamine-containing glycoprotein. The glycan bead may be selected from the group consisting of an agarose bead and a sepharose bead. The sample may comprise at least one selected from the group consisting of cultured cell lines, cells obtained from a subject, a tissue obtained from a subject, and serum obtained from a subject. The sample may further comprise peptides that are not specific to the binding site, wherein contacting the test agent with the sample provides additional complexes, in which one or more peptides are bound to at least one of the L4-PHA moiety and the glycan bead of the first complex at one or more locations other than the binding site.
Another aspect of the invention provides a diagnostic method for at least one of tumorigenesis and cancer metastasis. The method comprises: the foregoing method of analyzing a sample to determine a level of a β1,6-N-acetylglucosamine-containing glycoprotein; and determining if the level is indicative of at least one of tumorigenesis and cancer metastasis.
A further aspect of the invention provides a kit for determining a level of a β1,6-N-acetylglucosamine-containing glycoprotein in a sample. The kit comprises: a first complex comprising a glycan bead, an phytohemagglutinin-L4 (L4-PHA) moiety and a bridge linking between the glycan bead and the L4-PHA moiety, wherein the L4-PHA moiety may comprise a binding site specific to β1,6-N-acetylglucosamine, wherein the bridge may comprise a ligand and a ligand receptor engaged with the ligand, wherein the ligand is attached to one of the L4-PHA moiety and the glycan bead, wherein the ligand receptor is attached to the other of the L4-PHA moiety and the glycan bead; and wherein the first complex is configured to contact with a sample comprising a β1,6-N-acetylglucosamine-containing glycoprotein such that the first complex binds with the β1,6-N-acetylglucosamine-containing glycoprotein at the binding site to form a second complex, which may comprise the glycan bead, the L4-PHA moiety and the β1,6-N-acetylglucosamine-containing glycoprotein in a single entity.
The foregoing kit may further comprise: a denaturing agent configured for use in disassociating the ligand from the ligand receptor. The ligand may comprise a biotin, and the ligand receptor may comprise an avidin. The glycan bead may be selected from the group consisting of an agarose bead and a sepharose bead. The sample may comprise at least one selected from the group consisting of cultured cell lines, cells obtained from a subject, a tissue obtained from a subject, and serum obtained from a subject.



BRIEF DESCRIPTION OF DRAWINGS
FIG. 1 illustrates the structure of N-linked glycan linkages formed by various glycosyltransferases and L-PHA-binding β1,6-N-acetylglucosamine moiety.
FIG. 2 schematizes the procedures described in Example 1.
FIG. 3 shows the proteins identified according to the method described in Example 1, indicating that many of non-glycoproteins, but not a positive control TIMP-1, were detected.
FIG. 4 schematizes the procedures described in Example 2.
FIG. 5 shows the proteins identified according to the method described in Example 2, indicating that relatively more glycoproteins were detected with low score values and TIMP-1 was not detected still.
FIG. 6 schematizes the procedures described in Example 3.
FIG. 7 is one of the results derived from the method described in Example 3, indicating that many of glycoproteins including TIMP-1 were detected with significant score values.
FIG. 8 shows the proteins that are commonly identified through the method in Example 3 and the previous lectin blot analysis.
FIG. 9 shows the proteins that are identified through the method in Example 3, but not through the previous lectin blot analysis.
FIG. 10 is the comparative result of Example 2 and Example 3, indicating that a mass peak was detected at the retention time of 34.36 min. only through the method of Example 3.
FIG. 11 is a result of the multiple reaction monitoring (MRM) experiment, indicating that a TIMP-1 peptide was detected only in the Example 3.



DETAILED DESCRIPTION OF EMBODIMENTS
The object of the present invention is to provide a sensitive method for identifying glycoproteins acquiring changed glycan structures, termed aberrant glycoproteins, associated with tumorigenesis and cancer metastasis.
Another object of the present invention is to detect and identify aberrant glycoproteins involved in tumorigenesis and cancer metastasis by a simpler method.
For these objects, the inventors have developed the procedure for the detection of aberrant glycoproteins carrying β1,6-N-acetylglucosamine by probing them using L-PHA, a lectin recognizing N-linked glycoproteins with β1,6-N-acetylglucosamine moiety.
The present invention allows to detect even sparse proteins by providing methods in which aberrant glycoproteins carrying β1,6-N-acetylglucosamine involved in tumorigenesis and cancer metastasis are enriched by lectin precipitation. And, the present invention can be applied to every other cancer and to bio-materials including urine and blood.
The present invention provides the analytical method for detecting aberrant glycosylation involved in tumorigenesis and cancer metastasis using lectin precipitation and a list of aberrant glycoproteins as marker candidates for cancer diagnosis.
The present invention is on the sensitive analytical method for identifying glycoproteins carrying an aberrant glycosylation associated with tumorigenesis and cancer metastasis through lectin precipitation.
The applicable cancer type is selected from a group including colon, gastric, lung, liver, cervix, breast, and pancreatic cancer, but is not restricted to the mentioned cancer and can be extended to every cancer type.
The present invention provides a sensitive analytical method for identifying N-linked glycoproteins acquiring β1,6-N-acetylglucosamine moiety from cancer cells. GnT-V that catalyzes the formation of β1,6-N-acetylglucosamine is widely expressed in the various cancer tissues and thus involved the pathology. As β1,6-N-acetylglucosamine is recognized by phytohemagglutinin-L4 (abbreviated as “L4-PHA” or “L-PHA” hereinafter), biotin-labeled L-PHA can be noncovalently conjugated to avidin-agarose beads. The complexes can be, in turn, used to enrich β1,6-N-acetylglucosamine-carrying glycoproteins from protein preparations.
The present invention provides a method for the identification of sparse proteins in which 1,6-N-acetylglucosamine-carrying glycoproteins are trypsinized and subjected to the amino acid sequencing using 7-Teslar Fourier Transform Ion Cyclotron Resonance (FTICR) mass spectrometry.
One aspects of the invention provides a glycoprotein analyzing method containing:
Conjugating ligand-bound L4-PHA with a ligand receptor-attached glycan beads to form L4-PHA-glycan bead complex;
Reacting a sample with the said L4-PHA-glycan bead complex to get glycoproteins;
Running the said glycoproteins by gel electrophoresis;
In-gel digesting the resulted gel containing the said glycoproteins to peptides; and
Analyzing the digested peptides by mass spectrometry.
Another aspect of the invention provides the above method, wherein the glycan beads is selected from a group consisting of agarose beads and sepharose beads.
Another aspect of the invention provides the above method, wherein the ligand and the ligand receptor are biotin and avidin.
Another aspect of the invention provides the above method, wherein the sample is native form or denatured form.
Another aspect of the invention provides the above method, wherein the denatured form is generated by at least one selected from a group consisting of β-mercaptoethanol, iodoacetic acid and iodoacetamide.
Another aspect of the invention provides a detection method for glycoproteins that shows a difference in the glycan structure with respect to β1,6-N-acetylglucosamine by respectively adding control and experimental cultured cell lines to L4-PHA-glycan bead complex which is made by conjugating ligand-bound L4-PHA with a ligand receptor-attached glycan beads.
Another aspect of the invention provides a detection method for glycoproteins that shows a difference in the glycan structure with respect to β1,6-N-acetylglucosamine by respectively adding normal sera and experimental sera to L4-PHA-glycan bead complex which is made by conjugating ligand-bound L4-PHA with a ligand receptor-attached glycan beads.
Another aspect of the invention provides an identification method that provides a basis for validation of previously discovered cancer biomarker candidates with a minimal interference by highly abundant serum proteins like albumin, globulin, and transferrin, and can be combined with SISCAPA method (Stable Isotope Standards and Capture by Anti-peptide Antibodies: Pearson et al, 2004, J. Proteome Res. 3, 235-44) for maximizing the validation efficiency.
Cancer metastasis arises from dysfunctions in the cell recognition and adhesion, and many of membrane or secreted proteins are involved in the processes, which indicates that biofluids like blood and urine in which a potential biomarker may exist can be used as source of biomarker detection. To find a colon cancer-specific biomarker, The present inventors performed a glycomics study, where GnT-V gene was stably transfected into WiDr, a colon cancer cell line with low expression level of GnT-V. Proteins from the cultured media was resolved on 2-DE gels, which were used for staining with Coomassie Brilliant Blue or lectin blot analysis, and proteins showing differential glycan structures were selected between parental and transfectant WiDr cells (Table 1). However, lectin blot analysis itself has a feasibility of non-specific interaction or implications of contaminant proteins in gels, which requires additional confirmation steps. Moreover, 2-DE gels have a limited resolution capacity and thus sparse proteins are difficult to identify under the gel-based systems. To overcome those limitations, the inventors adopted a method enabling to detect directly β1,6-N-acetlyglucosaminylated glycoproteins using a specific lectin.












TABLE 1








Sequence




Accession

Peptides
Coveragea
Total


gi NO.
Identities
matched
(%)
Scoreb
Mr/pIc




















177836
α-1-antitrypsin
8
31.1
380
46.7/5.5


532198
Angiotensinogen
5
14.6
237
53.2/5.8


123081
-hexosaminidase chain
3
5.0
104
63.1/6.3



precursor


4503143
Cathepsin D preproprotein
8
23.5
459
44.6/6.1


3650498
Cathepsin X precursor
7
28.0
291
33.9/7.1


230581
Chain H, Immunoglobulin G1
6
17.9
314
49.7/8.5


21617867
Dipeptidyl aminopeptidase II
4
8.9
169
54.3/5.9


38327632
Discoidin receptor tyrosine
2
3.1
96
97.2/6.1



kinase isoform b


4758116
Dystroglycan 1 precursor
2
3.0
140
97.6/8.7


77416865
Granulins precursor
4
7.4
182
63.5/6.4


5729877
Heat shock 70 kDa protein 8
9
17.0
278
70.9/5.4



isoform 1


20149594
Heat shock 90 kDa protein 1,
7
11.3
229
83.3/5.0



beta


11602963
Heparan sulfate proteoglycan
5
2.2
175
466.6/6.0 



perlecan


4504371
Hexosaminidase A preproprotein
8
17.0
470
60.7/5.0


106586
Ig kappa chain V-III
2
10.7
124
23.1/5.8


1944352
IgG Fc binding protein
5
3.2
242
572.1/5.1 


14583014
laminin receptor-like protein 5
2
9.2
116
33.0/4.8


2842759
Legumain precursor
3
10.4
110
49.4/6.1


4557747
Met proto-oncogene precursor
11
9.1
512
155.5/7.0 


4503899
N-acetylgalactosamine-6-
5
14.9
309
58.0/6.3



sulfatase


4504061
N-acetylglucosamine-6-sulfatase
9
17.2
469
62.0/8.6


4505375
Neogenin homolog 1
5
4.7
248
160.0/6.1 


32485152
Prolyl 4-hydroxylase
5
15.2
247
84.8/5.3


11386147
Prosaposin
8
19.9
392
58.1/5.1


4505989
Protective protein for -
3
6.7
127
54.5/6.2



galactosidase


729008
Protein tyrosine kinase 6
3
5.1
76
101.1/6.4 


15826840
Protein tyrosine kinase 7
9
11.5
477
118.4/6.7 


5231228
Ribonuclease T2 precursor
5
22.6
247
29.5/6.7


11545839
Serine protease 22
2
11.0
117
33.7/7.6


135850
Tissue inhibitor of
2
7.2
102
24.2/8.5



metalloproteinase-1


120749
Tumor-associated calcium signal
2
11.8
163
34.9/7.4



transducer 1 precursor


4507677
Tumor rejection antigen-1
15
19.3
440
92.5/4.8



(gp96)


38026
Zn--2-glycoprotein
10
40.4
361
34.7/5.7





aSequence coverage refers to the percentage of peptides that was identified by mass spectrometer.


bTotal score is a sum of the score values obtained from each of an individual peptide. Score is −10 × Log (P), where P is the probability that the observed match is a random event; it is based on NCBInr database using the MASCOT searching program as MS/MS data.


cMolecular weight (Mr) and isoelectric point (pI) are theoretical values where glycan residues were not considered for the calculations.






Although L-PHA can bind to β1,6-N-acetylglucosaminylated glycoproteins with a high specificity, it is difficult to detach the bound proteins due to an unavailability of the elution method. To solve the problem, the inventors have the L-PHA-bound proteins run on an SDS-PAGE gel minimally, and the gels were sliced and trypsinized for protein identifications.
Various aspects and embodiments of the present invention will be explained in more detail with reference to the following examples.
Example 1
Enrichment of β1,6-N-Acetylglucosaminylated Glycoproteins Using a Lectin
WiDr:mock cells with a low GnT-V expression level and GnT-V transfectant WiDr:GnT-V were established as model cell lines and conditioned serum-free media were collected from the cell lines. As cancer metastasis has been known to arise from dysfunctions in the cell recognition and adhesion (Egeblad et al., 2002, Nature Rev. 2:161-174; Kannagi et al., 2004, Cancer Sci. 95(5):377-384), and many of membrane or secreted proteins are involved in the processes, β1,6-N-acetylglucosaminylated glycoproteins by GnT-V were purified from the conditioned media. The collected media were concentrated and 1 mg of proteins were allowed to bind to avidin-agarose beads to preclear non-specifically bound proteins. The pre-cleared proteins were allowed to interact with L-PHA-biotin-avidin-agarose beads complexes overnight at 4° C. Though mannose-1,6-N-acetylglucosamine may contribute to detaching the L-PHA bound proteins, the use of the disaccharide is costly and the efficacy has not been demonstrated. Some groups have attempted to detach by acidic elution method but the method has not been demonstrated either and low pH may do damage to the protein integrity. For the reasons, the proteins were digested under the conditions where proteins were bound to the complexes. For this, the protein complexes were washed with excess volumes of PBS buffer and trypsinized with 10 U of trypsin (Promega) overnight at 37° C. The digested peptides were extracted with distilled water and acetonitrile, dried under vacuo and mass-analyzed on a 7 Testla FTICR/LTQ mass spectrometer. Proteins were identified from the peptide sequences using Mascot search program (ver. 2.0) (FIGS. 2 & 3).
Database search was done against NCBInr 20051212 (taxonomy; human, entries; 103,913 human sequence entries). As a result, peptides are not effectively sequenced, which are thought to be due to a poor digestion of intact proteins by trypsin. TIMP-1 has previously been identified to be a target for GnT-V and the changed glycan structures were determined by mass spectrometry, which set TIMP-1 as a reference molecule. However, TIMP-1 was not identified in this method and many non-glycoproteins were identified instead.
Example 2
Protein Reduction and Desalting Prior to the Enrichment of β1,6-N-Acetylglucosaminylated Glycoproteins Using a Lectin
To reduce a non-specific interaction seen in Example 1 and enhance a sensitivity, proteins from the collected media were reduced by 1% (v/v) β-mercaptoethanol and the unreacted β-mercaptoethanol and salts were removed on a gel-filtration column (FIG. 4). One mg of proteins were precipitated and identified as described in Example 1. The result shows that more glycoproteins were identified, however, with low score value, and TIMP-1 was not identified either.
Example 3
Maximized Protein Digestion in SDS-PAGE Gels and Identification of β1,6-N-Acetylglucosaminylated Glycoproteins Following the Lectin Precipitation
Proteins collected from the cultured media as described in Example 1 were reduced by 1% (v/v) β-mercaptoethanol, the unreacted β-mercaptoethanol and salts were removed on a gel-filtration column as described in Example 2. One mg of proteins were precleared with avidin-agarose beads for an hour and the precleared proteins were allowed to bind to L-PHA-biotin-avidin-agarose beads complex overnight at 4° C. After extensive washing with PBS, the bound proteins were separated from the beads complex by adding 1×SDS-PAGE denaturation buffer and boiling briefly. Proteins were resolved on an 8% SDS-PAGE gel and tryptic-digested in gels. The digested peptides were eluted from the gel, resolved using Agilent 1100 Nanoflow systems and sequence-analyzed on a Surveyor system connected to a 7-T FT-LTQ mass spectrometer (Thermo Electron). Peptides were bound and separated on a 10 cm silica column (75 mm) packed with ReproSil-Pur C18-AQ resin (Ammerbuch-Entringen). Peptide mixtures were loaded onto a 100 mm-C18 column (5 μm) by an autosampler (Surveyor) at a flow rate of 20 ml/min. The mobile phases, A and B, were composed of 0% and 100% ACN, respectively, each containing 0.1% formic acid. The gradient began at 5% B for 15 min, was ramped to 20% B for 3 min, to 50% for 47 min, and finally to 95%. The eluted peptides were directly electrosprayed into the mass spectrometer. The mass spectrometer was controlled by Xcalibur software (ThermoElectron Corp., Version 1.4SR1). FIG. 7 represents one of the results. This example allowed to 1) identify glycoproteins with significant score values (P<0.05), 2) detect TIMP-1 as in FIG. 7, 3) confirm the proteins that were previously identified through the lectin blot-based identification method (FIG. 8), and 4) detect proteins showing a low expression level with high score values (FIG. 9).
Example 4
Confirmation of the Lectin Precipitation-Based Protein Identification by Mass Spectrometry
To compare Example 2 and Example 3, a readily-detected peptide of TIMP-1, GFQALGDAADIR (SEQ ID NO:1), was monitored by mass spectrometry. As shown in FIG. 10, GFQALGDAADIR (SEQ ID NO:1) shows a molecular weight of 1,232 Da and 617.31 m/z in the −2 charge state. A peptide was detected at the retention time of 34 min. in the Example 3, but not in Example 2 and the peptide sequence was found to be GFQALGDAADIR (SEQ ID NO:1). In addition, FIG. 3 shows a parent ion of a peptide detected at m/z 617.31 and a fragment ion at m/z 717.36 in the Example 3, none of which were detected in the Example 2 presumably due to a poor tryptic digestion and extraction. The inventors concluded from those results that Example 3 is an optimized method for identifying 1,6-N-acetylglucosaminylated glycoproteins.
Therefore, the present invention provides far more sensitive method than the 2-DE-based method for identifying sparse proteins showing glycosylation changes.
The present invention enables to diagnose cancer with ease at early stage by differentiating the levels and structures of glycoproteins between normal and experimental samples.

## Claims

1. A method of analyzing a sample to determine a level of a β1,6-N-acetylglucosamine-containing glycoprotein, the method comprising:
providing a test agent comprising a first complex, wherein the first complex comprises a glycan bead and an phytohemagglutinin-L4 (L4-PHA) moiety connected to the glycan bead, wherein the L4-PHA moiety comprises a binding site specific to β1,6-N-acetylglucosamine;
providing a sample comprising a β1,6-N-acetylglucosamine-containing glycoprotein;
contacting the test agent with the sample to provide a test mixture, in which the β1,6-N-acetylglucosamine-containing glycoprotein binds with the first complex at the binding site, thereby forming a second complex in the mixture, wherein the second complex comprises the glycan bead, the L4-PHA moiety and the β1,6-N-acetylglucosamine-containing glycoprotein as a single entity;
heating and applying a denaturing agent to the second complex to provide a denatured mixture, in which the β1,6-N-acetylglucosamine-containing glycoprotein is disassociated from the L4-PHA moiety and the glycan bead;
separating the glycan bead from the denatured mixture to provide the β1,6-N-acetylglucosamine-containing glycoprotein substantially free of the glycan bead;
subsequently fragmentizing the β1,6-N-acetylglucosamine-containing glycoprotein into smaller fragments; and
analyzing the fragments using a mass spectrometric procedure to determine a level of the β1,6-N-acetylglucosamine-containing glycoprotein in the sample.

2. The method of claim 1, further comprising:
collecting, from the test mixture, compounds and complexes that comprise a glycan bead while substantially excluding other compounds and complexes that do not contain a glycan bead, wherein the collected compounds and complexes comprise the second complex.

3. The method of claim 1, wherein the first complex further comprises a bridge interconnecting the glycan bead and the L4-PHA moiety, wherein the bridge comprises a ligand receptor and a ligand engaged with the ligand receptor, wherein the ligand is attached to the L4-PHA moiety, wherein the ligand receptor is attached to the glycan bead.

4. The method of claim 3, wherein heating and applying a denaturing agent causes to disengage the ligand from the ligand receptor, thereby further disassociating the L4-PHA moiety from the glycan bead, whereby the denatured mixture comprises the β1,6-N-acetylglucosamine-containing glycoprotein, the L4-PHA moiety and the glycan bead as separate entities.

5. The method of claim 4, wherein separating comprises running an electrophoresis in a gel medium, thereby separating the glycan bead from the β1,6-N-acetylglucosamine-containing glycoprotein and the L4-PHA moiety in the denatured mixture.

6. The method of claim 5, wherein fragmentizing comprises contacting an enzymatic agent with the β1,6-N-acetylglucosamine-containing glycoprotein and the L4-PHA moiety.

7. The method of claim 1, wherein the first complex further comprises a bridge interconnecting the glycan bead and the L4-PHA moiety, wherein the bridge comprises a biotin and an avidin engaged with the biotin, wherein the biotin is attached to the L4-PHA moiety, wherein the avidin is attached to the glycan bead.

8. The method of claim 1, wherein separating comprises running an electrophoresis in a gel medium, thereby separating the glycan bead from the β1,6-N-acetylglucosamine-containing glycoprotein.

9. The method of claim 1, wherein fragmentizing comprises contacting an enzymatic agent with the β1,6-N-acetylglucosamine-containing glycoprotein.

10. The method of claim 9, wherein the enzymatic agent is applied to the gel medium containing the β1,6-N-acetylglucosamine-containing glycoprotein.

11. The method of claim 1, wherein the glycan bead is selected from the group consisting of an agarose bead and a sepharose bead.

12. The method of claim 1, wherein the sample comprises at least one selected from the group consisting of cultured cell lines, cells obtained from a subject, a tissue obtained from a subject, and serum obtained from a subject.

13. The method of claim 1, wherein the sample further comprises peptides that are not specific to the binding site, wherein contacting the test agent with the sample provides additional complexes, in which one or more peptides are bound to at least one of the L4-PHA moiety and the glycan bead of the first complex at one or more locations other than the binding site.

14. The method of claim 1, wherein the first complex further comprises a bridge interconnecting the glycan bead and the L4-PHA moiety, wherein the bridge comprises a ligand receptor and a ligand engaged with the ligand receptor, wherein the ligand is attached to the glycan bead, wherein the ligand receptor is attached to the L4-PHA moiety.

15. The method of claim 1, wherein the first complex further comprises a bridge interconnecting the glycan bead and the L4-PHA moiety, wherein the bridge comprises a biotin and an avidin engaged with the biotin, wherein the biotin is attached to the glycan bead, wherein the avidin is attached to the L4-PHA moiety.