U.S. patent application number 13/045575 was filed with the patent office on 2011-08-11 for cspcna isoform modifications and uses thereof.
This patent application is currently assigned to Indiana University Research and Technology Corporation. Invention is credited to Robert J. HICKEY, Derek J. HOELZ, Linda H. MALKAS.
Application Number | 20110195510 13/045575 |
Document ID | / |
Family ID | 37116243 |
Filed Date | 2011-08-11 |
United States Patent
Application |
20110195510 |
Kind Code |
A1 |
HOELZ; Derek J. ; et
al. |
August 11, 2011 |
csPCNA Isoform Modifications And Uses Thereof
Abstract
Methods and compositions to detect the presence of csPCNA
isoform by identifying one or more posttranslational modifications
are disclosed. Methods to identify csPCNA isoform through
posttranslational modifications including methylesterification
levels are disclosed.
Inventors: |
HOELZ; Derek J.; (Bangor,
ME) ; HICKEY; Robert J.; (Indianapolis, IN) ;
MALKAS; Linda H.; (Indianapolis, IN) |
Assignee: |
Indiana University Research and
Technology Corporation
Indianapolis
IN
|
Family ID: |
37116243 |
Appl. No.: |
13/045575 |
Filed: |
March 11, 2011 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11993252 |
Feb 15, 2008 |
7932023 |
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PCT/US06/24774 |
Jun 26, 2006 |
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13045575 |
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60694159 |
Jun 27, 2005 |
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Current U.S.
Class: |
436/86 ; 530/324;
530/326; 530/327; 530/328; 530/329; 530/330 |
Current CPC
Class: |
G01N 33/57484 20130101;
C07K 14/4738 20130101; G01N 33/6875 20130101 |
Class at
Publication: |
436/86 ; 530/330;
530/329; 530/328; 530/327; 530/326; 530/324 |
International
Class: |
G01N 33/48 20060101
G01N033/48; C07K 7/06 20060101 C07K007/06; C07K 7/08 20060101
C07K007/08; C07K 14/00 20060101 C07K014/00 |
Goverment Interests
GOVERNMENT RIGHTS
[0002] This invention was made with government support under grant
number DAMD17-02-1-0467 awarded by the Army Medical Research and
Material Command The U.S. Government has certain rights in the
invention
Claims
1. A method of diagnosing or prognosing malignancy, the method
comprising: detecting a post-translational modification comprising
a methyl ester on one or more of 16 aspartic acid or glutamic acid
residues corresponding to the amino acid positions 3, 85, 93, 94,
104, 109, 115, 120, 132, 143, 174, 189, 201, 238, 256, and 259 of
SEQ ID NO: 30 in a biological sample suspected of containing a
csPCNA isoform; comparing the levels of methyl esters on the csPCNA
isoform with a nonmalignant isoform of PCNA, wherein the csPCNA
isoform has a lower level of methyl esterification than the
nonmalignant isoform of PCNA; and diagnosing or prognosing
malignancy based on detection of csPCNA in the biological
sample.
2. The method of claim 1, wherein the biological sample is a bodily
fluid.
3. The method of claim 2, wherein the bodily fluid is selected from
blood, plasma, lymph, serum, pleural fluid, spinal fluid, saliva,
sputum, urine, gastric juice, pancreatic juice, ascites fluid,
synovial fluid, milk, and semen.
4. The method of claim 1, wherein the biological sample is a tissue
sample.
5. The method of claim 4, wherein the tissue is selected from
breast, prostate, lung, colon, epithelial, connective, cervical,
esophageal, brain, thymus, thyroid, pancreas, testis, ovary,
intestine, bladder, stomach, soft tissue sarcomas, osteosarcoma,
leukemia, lymphoma, carcinoma, adenocarcinoma, placenta, fibrous,
germ cell tissue, and extracts thereof.
6. The method of claim 1, wherein the methyl ester present on one
or more of the 16 aspartic acid or glutamic acid residues
corresponds to the peptides with modified amino acid residues
selected from TABLE-US-00004 MFE.sub.mAR; (SEQ ID NO: 1)
IE.sub.mDEEGS; (SEQ ID NO: 2) IEDEE.sub.mGS; (SEQ ID NO: 3)
VSDYE.sub.mMK; (SEQ ID NO: 4) MPSGE.sub.mFAR; (SEQ ID NO: 5)
LSQTSNVD.sub.mK; (SEQ ID NO: 6) CAGNE.sub.mDIITLR; (SEQ ID NO: 7)
FSASGE.sub.mLGNGNIK; (SEQ ID NO: 8) AEDNADTLALVFEAPNQE.sub.mK; (SEQ
ID NO: 9) AE.sub.mDNADTLALVFEAPNQEK; (SEQ ID NO: 10)
AED.sub.mNADTLALVFEAPNQEK; (SEQ ID NO: 11)
AEDNADTLALVFE.sub.mAPNQEK; (SEQ ID NO: 12)
LMD.sub.mLDVEQLGIPEQEYSCVVK; (SEQ ID NO: 13)
ATPLSSTVTLSMSADVPLVVE.sub.mYK; (SEQ ID NO: 14)
LSQTSNVDKEEEAVTIEMNE.sub.mPVQLTFALR; (SEQ ID NO: 15) and
LMDLDVEQLGIPEQE.sub.mYSCVVK, (SEQ ID NO: 31)
wherein E.sub.m represents a methylesterified glutamic acid residue
and D.sub.m represents a methylesterified aspartic acid
residue.
7. The method of claim 1, wherein the detection of csPCNA isoform
is performed using a mass spectrometric analysis.
8. The method of claim 7, wherein the mass spectrometric analysis
is liquid chromatography (LC) mass spectrometric (MS) analysis.
9. The method of claim 7, wherein the mass spectrometric analysis
of a csPCNA-derived peptide results in a 14 Da mass shift as
compared to a corresponding unmodified peptide.
10. A modified proliferating cell nuclear antigen (PCNA) peptide
comprising an amino acid sequence selected from the group
consisting of: TABLE-US-00005 MFE.sub.mAR; (SEQ ID NO: 1)
IE.sub.mDEEGS; (SEQ ID NO: 2) IEDEE.sub.mGS; (SEQ ID NO: 3)
VSDYE.sub.mMK; (SEQ ID NO: 4) MPSGE.sub.mFAR; (SEQ ID NO: 5)
LSQTSNVD.sub.mK; (SEQ ID NO: 6) CAGNE.sub.mDIITLR; (SEQ ID NO: 7)
FSASGE.sub.mLGNGNIK; (SEQ ID NO: 8) AEDNADTLALVFEAPNQE.sub.mK; (SEQ
ID NO: 9) AE.sub.mDNADTLALVFEAPNQEK; (SEQ ID NO: 10)
AED.sub.mNADTLALVFEAPNQEK; (SEQ ID NO: 11)
AEDNADTLALVFE.sub.mAPNQEK; (SEQ ID NO: 12)
LMD.sub.mLDVEQLGIPEQEYSCVVK; (SEQ ID NO: 13)
ATPLSSTVTLSMSADVPLVVE.sub.mYK; (SEQ ID NO: 14)
LSQTSNVDKEEEAVTIEMNE.sub.mPVQLTFALR; (SEQ ID NO: 15) and
LMDLDVEQLGIPEQE.sub.mYSCVVK; (SEQ ID NO: 31)
wherein E.sub.m represents a methylesterified glutamic acid residue
and D.sub.m represents a methylesterified aspartic acid
residue.
11. The modified peptide of claim 10, wherein the peptides are
post-translationally modified.
12. The modified peptide of claim 10, wherein the peptides are
exposed to a protease digestion step.
13. The modified peptide of claim 10, wherein the peptides are
synthetic.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a divisional application of and claims
priority to U.S. application Ser. No. 11/993,252, filed Feb. 15,
2008, which is a U.S. Nationalization of PCT/US06/24774, filed Jun.
26, 2006, which claims benefit of U.S. Ser. No. 60/694,159, filed
Jun. 27, 2005, the entire disclosures of which are incorporated by
reference herein.
FIELD
[0003] The present disclosure relates to detection of malignant
cells involving the use of modifications to a cancer specific
protein.
BACKGROUND
[0004] One of the least understood and most complex disease
processes is the transformation that occurs as a cell becomes
malignant. This process involves both genetic mutations and
proteomic transformations, the result of which, allows the cell to
escape normal controls; preventing inappropriate cell division.
Cancer cells share some common attributes. Most cancer cells
proliferate outside of the normal cell cycle controls, exhibit
morphological changes and exhibit various biochemical disruptions
to cellular processes.
[0005] Cancer is usually diagnosed when a tumor becomes visible
well after the first on-set of cellular changes. Many cancers are
diagnosed after a biopsy sample is examined by histology for
morphologic abnormalities, evidence of cell proliferation and
genetic irregularities. Effective treatment for malignancy often
depends on the ability to detect reliably, the presence of
malignant cells at early stages of a disease so that an effective
treatment can begin at a stage when the disease is more susceptible
to such treatment. Thus, there is a need to be able to reliably
detect a potentially malignant cell that has not progressed to the
histological stage recognized as malignant, but which can progress
to a malignant state. There is also a need for a rapid, minimally
invasive technique that can reliably detect or treat malignant
cells or potentially malignant cells.
[0006] Proliferating cell nuclear antigen (PCNA) is a 29 kDa
nuclear protein and its expression in cells during the S and G2
phases of the cell cycle, makes the protein a good cell
proliferation marker. It has also been shown to partner in many of
the molecular pathways responsible for the life and death of the
cell. Its periodic appearance in S phase nuclei suggested an
involvement in DNA replication. PCNA was later identified as a DNA
polymerase accessory factor in mammalian cells and an essential
factor for SV40 DNA replication in vitro. In addition to
functioning as a DNA sliding clamp protein and a DNA polymerase
accessory factor in mammalian cells, PCNA interacts with a number
of other proteins involved in transcription, cell cycle
checkpoints, chromatin remodeling, recombination, apoptosis, and
other forms of DNA repair. Besides being diverse in action, PCNA's
many binding partners are linked by their contributions to the
precise inheritance of cellular functions by each new generation of
cells. PCNA may act as a master molecule that coordinates
chromosome processing.
[0007] PCNA is also known to interact with other factors like
FEN-1, DNA ligase, and DNA methyl transferase. Additionally, PCNA
was also shown to be an essential player in multiple DNA repair
pathways. Interactions with proteins like the mismatch recognition
protein, Msh2, and the nucleotide excision repair endonuclease,
XPG, have implicated PCNA in processes distinct from DNA synthesis.
Interactions with multiple partners generally rely on mechanisms
that enable PCNA to selectively interact in an ordered and
energetically favorable way.
[0008] Clues to a mechanism of PCNA's functions were initially
uncovered through investigation of the DNA synthesome, a
multiprotein DNA replication complex present in mammalian cells.
Studies examining the synthetic activity of the DNA synthesome
identified an increased error rate in malignant cells when compared
to non-malignant cells. These results suggest that a structural
alteration to one or more components of the DNA synthesome in
malignant cells has occurred. 2D-PAGE immunoblot analysis of PCNA,
an essential component of the DNA synthesome, revealed two distinct
isoforms with vastly different isoelectric points (pIs). One PCNA
isoform displayed a significantly basic pI and was present in both
malignant and non-malignant cells. The other isoform had an acidic
pI and was found exclusively in malignant cells. Because of its
presence only in malignant cells, this isoform was termed the
cancer-specific isoform or csPCNA, and the post-translational
alteration that is responsible for PCNA's altered 2D-PAGE migration
pattern remains undetermined.
[0009] Some labeling studies with PCNA suggested that the migration
of PCNA was most likely not due to alterations such as
phosphorylation, acetylation, glycosylation, or sialyzation.
Conflicting studies have surfaced attempting to identify
post-translational modifications to PCNA. For example, the
phosphorylation of PCNA was reported to affect its binding to sites
of DNA synthesis. Another study claimed that PCNA was, after all,
not phosphorylated but acetylated. In addition to these studies,
analysis of yeast PCNA has shown it to be the target of
ubiquitination in response to DNA damage and sumoylation in the
absence of damage. Due to the diverse and conflicting structural
evidence for PCNA, it is difficult to identify which modifications,
if any, are responsible for the appearance and functions of csPCNA
isoform.
[0010] Therefore, identification of the correct post-translational
modifications of csPCNA is desirable to develop diagnostic methods
and also to develop therapeutics based on the interactions of
csPCNA with its partners. Malignant cancer cells express an isoform
of PCNA termed cancer specific PCNA (csPCNA) and non-malignant
cells express an isoform termed non-malignant PCNA (nmPCNA).
Effective compositions and methods to distinguish the two isoforms
are needed for diagnosis and treatment of cancers.
SUMMARY
[0011] Novel post-translational modifications of csPCNA are
identified. Methyl esterification of csPCNA is identified. A
2D-PAGE/liquid chromatography tandem mass spectrometry (LC-MS/MS)
approach was used to analyze the csPCNA isoform and to identify
methyl esterifications present on csPCNA. The methyl esterification
modifications were localized to specific glutamic and aspartic acid
residues.
[0012] A structural analysis of a single acidic PCNA isoform
(csPCNA) isolated from breast cancer cells by two-dimensional
electrophoresis (2D-PAGE) and liquid chromatography tandem mass
spectrometry (LC-MS/MS) is disclosed herein. The methyl esters
localized to 16 specific glutamic and aspartic acid residues of
csPCNA. The methyl esterification of csPCNA represents a novel type
of post-translational modification in mammalian cells that are
relevant in addressing some of PCNA's diverse functions.
[0013] A method of detecting a cancer specific proliferating cell
nuclear antigen (csPCNA) isoform in a biological sample includes
the steps of:
[0014] detecting a posttranslational modification comprising a
methyl ester on one or more amino acid residues of the csPCNA
isoform in the sample suspected of containing the csPCNA isoform;
and
[0015] determining the presence of the csPCNA isoform by comparing
the levels of methyl esters on the csPCNA isoform with a
nonmalignant isoform of PCNA.
[0016] Some of the biological samples includes a bodily fluid, such
as blood, plasma, lymph, serum, pleural fluid, spinal fluid,
saliva, sputum, urine, gastric juice, pancreatic juice, ascites
fluid, synovial fluid, milk, and semen.
[0017] A biological sample also includes a tissue sample such as
tissues obtained from, breast, prostrate, lung, colon, epithelial,
connective, cervical, esophageal, brain, thymus, thyroid, pancreas,
testis, ovary, intestine, bladder, stomach, soft tissue sarcomas,
osteosarcoma, leukemia, lymphoma, carcinoma, adenocarcinoma,
placenta, fibrous, germ cell tissue, and extracts thereof. Any
biological sample that is capable of containing csPCNA is suitable
for analysis.
[0018] In an aspect, the methyl ester is present on an aspartic
acid or on a glutamic acid or a combination thereof of the csPCNA
isoform. A methyl ester is present on one or more of the 16
aspartic acid or glutamic acid residues on the csPCNA isoform. The
methyl ester present on one or more of the 16 aspartic acid or
glutamic acid residues correspond to the amino acid positions with
reference to SEQ ID NO: 30 of 3, 85, 93, 94, 104, 109, 115, 120,
132, 143, 174, 189, 201, 238, 256, and 259 of csPCNA isoform. The
csPCNA-derived peptides that include the 16 aspartic acid or
glutamic acid modified residues are as follows:
[0019] MFE.sub.mAR (SEQ ID NO: 1);
[0020] IE.sub.mDEEGS (SEQ ID NO: 2);
[0021] IEDEE.sub.mGS (SEQ ID NO: 3);
[0022] VSDYE.sub.mMK (SEQ ID NO: 4);
[0023] MPSGE.sub.mFAR (SEQ ID NO: 5);
[0024] LSQTSNVD.sub.mK (SEQ ID NO: 6);
[0025] CAGNE.sub.mDIITLR (SEQ ID NO: 7);
[0026] FSASGE.sub.mLGNGNIK (SEQ ID NO: 8);
[0027] AEDNADTLALVFEAPNQE.sub.mK (SEQ ID NO: 9);
[0028] AE.sub.mDNADTLALVFEAPNQEK (SEQ ID NO: 10);
[0029] AED.sub.mNADTLALVFEAPNQEK (SEQ ID NO: 11);
[0030] AEDNADTLALVFE.sub.mAPNQEK (SEQ ID NO: 12);
[0031] LMD.sub.mLDVEQLGIPEQEYSCVVK (SEQ ID NO: 13);
[0032] ATPLSSTVTLSMSADVPLVVE.sub.mYK (SEQ ID: 14);
[0033] LSQTSNVDKEEEAVTIEMNE.sub.mPVQLTFALR (SEQ ID NO: 15); and
[0034] LMDLDVEQLGIPEQE.sub.mYSCVVK (SEQ ID NO: 31), wherein E.sub.m
represents a methylesterified glutamic acid residue and D.sub.m
represents a methylesterified aspartic acid residue.
[0035] In an aspect, the detection of csPCNA isoform is performed
using a mass spectrometric analysis, for example, by liquid
chromatography (LC) mass spectrometric (MS) analysis. Any suitable
method of detection of methyl esters or methylesterified amino acid
residues is applicable.
[0036] A mass spectrometric analysis of a csPCNA-derived peptide
results in a 14 Da mass shift as compared to a corresponding
unmodified peptide.
[0037] A method of diagnosing or prognosing malignancy, the method
includes the steps of: [0038] detecting cancer specific
proliferating cell nuclear antigen (csPCNA) isoform isoform in a
biological sample by identifying a posttranslational modification
state of csPCNA isoform that distinguishes the csPCNA isoform from
a nonmalignant PCNA (nmPCNA) isoform; and [0039] diagnosing
malignancy based on the detection of csPCNA in the biological
sample.
[0040] A posttranslational modification such as
methylesterification is detected on csPCNA and the
methylesterification levels on csPCNA versus nmPCNA are used in
determining malignancy.
[0041] A modified proliferating cell nuclear antigen (PCNA) peptide
includes an amino acid sequence selected from:
[0042] MFE.sub.mAR (SEQ ID NO: 1);
[0043] IE.sub.mDEEGS (SEQ ID NO: 2);
[0044] IEDEE.sub.mGS (SEQ ID NO: 3);
[0045] VSDYE.sub.mMK (SEQ ID NO: 4);
[0046] MPSGE.sub.mFAR (SEQ ID NO: 5);
[0047] LSQTSNVD.sub.mK (SEQ ID NO: 6);
[0048] CAGNE.sub.mDIITLR (SEQ ID NO: 7);
[0049] FSASGE.sub.mLGNGNIK (SEQ ID NO: 8);
[0050] AEDNADTLALVFEAPNQE.sub.mK (SEQ ID NO: 9);
[0051] AE.sub.mDNADTLALVFEAPNQEK (SEQ ID NO: 10);
[0052] AED.sub.mNADTLALVFEAPNQEK (SEQ ID NO: 11);
[0053] AEDNADTLALVFE.sub.mAPNQEK (SEQ ID NO: 12);
[0054] LMD.sub.mLDVEQLGIPEQEYSCVVK (SEQ ID NO: 13);
[0055] ATPLSSTVTLSMSADVPLVVE.sub.mYK (SEQ ID NO: 14);
[0056] LSQTSNVDKEEEAVTIEMNE.sub.mPVQLTFALR (SEQ ID NO: 15); and
[0057] LMDLDVEQLGIPEQE.sub.mYSCVVK (SEQ ID NO: 31), wherein E.sub.m
represents a methylesterified glutamic acid residue and D.sub.m
represents a methylesterified aspartic acid residue.
[0058] In one aspect, the modified peptides of csPCNA or PCNA are
posttranslationally modified. In another aspect, the modified
peptides of csPCNA or PCNA are exposed to a protease digestion
step. In another aspect, the modified peptides of csPCNA or nmPCNA
are synthetic.
[0059] In an aspect, a method of detecting a cancer specific
proliferating cell nuclear antigen (csPCNA) isoform in a biological
sample includes determining the overall methylesterification levels
of csPCNA and nmPCNA and determining that the biological sample has
csPCNA based on the methylesterification levels.
[0060] Additional features of the present disclosure will become
apparent to those skilled in the art upon consideration of the
following detailed description of embodiments exemplifying the best
mode of carrying out the subject matter of the disclosure as
presently perceived.
BRIEF DESCRIPTION OF THE DRAWINGS
[0061] FIG. 1 demonstrates identification of csPCNA from 2D-PAGE by
LC-MS/MS peptide characterization. (A) shows a representative
Coomassie blue stained 2D-PAGE gel of a MDA MB 468 cell nuclear
extract (2 mg). Multiple spots were chosen for proteolysis with
trypsin and identified by LC-MS/MS. csPCNA is identified (black
arrow) on the acidic side of the gel with an approximate pI of 4.6.
Three dimensional representation of the 2D-PAGE detects two spots
corresponding to csPCNA, a spot of modest abundance (black arrow),
and a more acidic spot of low abundance (white arrow) detected by
the 2D analysis software. Protein spots (i-v) other than PCNA that
were identified in the analysis are presented in Table I. (B) shows
base peak chromatogram of the peptides derived from the trypsin
digestion of csPCNA. (C) illustrates mass spectrum of a csPCNA
peptide eluting at 43.3 min Analysis of the tandem mass spectrum of
the 1038.7 m/z ion (D) identified it as a doubly charged peptide
corresponding to residues 92-110 of human PCNA (SEQ ID NO: 17). (E)
is mass spectrum showing the elution of a 1045.4 m/z ion at 43.74
min. The mass difference of the singly charged ions is twice the
difference of the doubly charged ion and the 1045.4 m/z ion
therefore displays a +14 Da mass shift. (F) shows tandem mass
spectrum of the 1045.4 m/z ion is nearly identical to the one in
part D except that all of the y-ions are shifted by 14 Da. The
shift in mass of only the b.sub.18-ion locates the additional 14 Da
on the glutamic acid at position 109 of csPCNA (SEQ ID NO: 17).
[0062] FIG. 2 shows creation of staggered peptide sequence maps of
csPCNA. (A) Representative base peak chromatograms showing the
elution of peptides derived from the cleavage of csPCNA with
trypsin (blue) (SEQ ID NO: 26), trypsin/CNBr (green) (SEQ ID NO:
27), GluC (red) (SEQ ID NO: 28), and AspN (black) (SEQ ID NO: 29).
(B) csPCNA maps of sequences identified by LC-MS/MS. The locations
of methyl esters are denoted (X.sub.m).
[0063] FIG. 3 shows that the C-terminal tail of PCNA is methyl
esterified at multiple sites. (A) Elution of three different
peptides (SEQ ID NOS: 16, 2, & 3, respectively) derived from
the C-terminal tail of csPCNA. The base peak chromatogram of csPCNA
digested with trypsin compared to the selected ion chromatograms of
the peptide IEDEEGS (SEQ ID NO: 16) (778.5 m/z) and the methyl
esterified IEDEEGS (SEQ ID NO: 16) peptides (792.5). The methyl
esterified peptides have an increased hydrophobicity and elute
later in the reversed-phase gradient. (B) Interpretation of the
tandem mass spectra for the unmodified peptide shows the
fragmentation of a singly charged peptide with the sequence IEDEEGS
(SEQ ID NO: 16). The neutral loss of water (-18 Da) is commonly
observed with many of the fragment ions. Additionally, a fragment
ion representing the neutral loss of water and CO group from the
y.sub.4-ion is observed at 373.9 m/z. (C) Tandem mass spectrum of
the 792.3 m/z ion from the peptide eluting first in the above
chromatogram. The b.sub.3-6-ions can be identified in the spectrum
and all are shifted by 14 Da but the y.sub.3 and y.sub.5-ions are
not shifted, suggesting that the modification lies on either the
leucine or glutamic acid of the N-terminus (peptide disclosed as
SEQ ID NO: 2). (D) Tandem mass spectrum of the 792.3 m/z ion from
the peptide eluting second in the separation. The b.sub.5 and
b.sub.6-ions contain the 14 Da shift as above, but the b.sub.3 and
b.sub.4 ions do not, consistent with the methyl ester on the
glutamic acid at position 5 in the peptide (peptide disclosed as
SEQ ID NO: 3).
[0064] FIG. 4 shows immunoblot of PCNA.
[0065] FIG. 5 shows an amino acid sequence of PCNA (1-261 amino
acids) (SEQ ID NO: 30).
DETAILED DESCRIPTION
[0066] Proliferating cell nuclear antigen (PCNA) protein is altered
in cancer cells. PCNA is a 28 kD protein with an electrophoretic
mobility equivalent to that of a 36 kDa protein. PCNA is an
accessory factor required by DNA polymerase 8 to mediate highly
efficient DNA replication activity. The DNA synthesome purified
from a malignant cell contains at least two forms of PCNA. The two
species of PCNA differ significantly in their overall charge. Thus,
an acidic, malignant or cancer specific, form of PCNA, csPCNA, and
a basic, nonmalignant or normal, form of PCNA, nmPCNA, can be
distinguished on a two-dimensional polyacrylamide gel.
[0067] The acidic csPCNA is expressed in malignant cell lines, such
as HeLa (human cervical carcinoma), Hs578T (breast carcinoma),
HL-60 (human promyelogenous leukemia), FM3A (mouse mammary
carcinoma), PC 10 (prostate carcinoma), LNCaP (prostate carcinoma),
LN99 (prostate carcinoma) MD-MB468 (human breast carcinoma), MCF-7
(breast carcinoma), KGE 90 (esophageal-colon carcinoma), KYE 350
(esophageal-colon carcinoma), SW 48 (esophageal-colon carcinoma)
and T98 (malignant glioma). The acidic csPCNA is also expressed in
malignant cells obtained from human breast tumors, prostate tumors,
brain tumors, human gastrointestinal or esophageal-colon tumors,
murine breast tumors and in human chronic myelogenous leukemia. The
acidic csPCNA is not detected in nonmalignant cell lines, such as
the breast cell lines Hs578Bst and MCF-10A, or in samples of
nonmalignant serum or tissue, such as breast.
[0068] An LC-MS/MS peptide characterization approach was used to
sequence a csPCNA isoform found in malignant cells. A novel type of
post-translational modification present on numerous residues of
csPCNA was identified. This modification, methyl esterification,
was present on 16 different aspartic acid and glutamic acid
residues in csPCNA. Unmodified amino acid sequence of PCNA is shown
in FIG. 5. These methyl esters were initially identified as 14 Da
shifts in peptide mass and were localized to either glutamic or
aspartic acid residues by tandem mass spectrometry. Relative
quantitation of the methyl esterified peptides indicated that
csPCNA proteins in malignant cells include several molecules
containing one or more methyl esters that occur at multiple
residues throughout the protein. Methyl esterification of specific
residues is likely to result in discrete conformational changes in
the protein, and these changes may promote and/or disrupt
protein/protein interactions.
[0069] The effects of methyl esterification on mammalian protein
functions are poorly understood. Much of the past research into
methyl esterification of mammalian proteins has focused on protein
aging and the repair of isoaspartyl residues by the enzyme protein
isoaspartate methyl transferase (PIMT). However, most methyl esters
present on csPCNA are found on glutamic acid residues and not
aspartic acid residues suggesting that the modification occurs via
an alternate pathway.
[0070] It is possible that methyl esterification of PCNA alters its
conformation and, in effect, hide and/or expose specific protein
binding sites and determines its function. LC-MS/MS sequence
analysis of recombinant PCNA was also performed and evidence for
methyl esterification was found. The methyl esterification found on
PCNA may therefore stabilize specific conformational states of an
otherwise disordered protein. Additionally, calculation of the
electrostatic potential of PCNA shows that the outer surface of the
PCNA trimer has a highly negative potential and an abundance of
glutamic and aspartic acid residues. Methylation of these residues
could therefore alter this potential and, in effect, change the
surface topology of the protein.
[0071] LC-MS/MS peptide characterization of a specific isoform,
csPCNA, resolved by 2D-PAGE is disclosed. Using a combination of
proteolytic approaches, staggered peptide sequence maps of csPCNA
were generated, identifying 100% of the csPCNA protein sequence by
LC-MS/MS. A novel post-translational modification present on csPCNA
was identified. Methyl esters appeared on at least one of 16
specific aspartic and/or glutamic acid residues in the csPCNA
isoform. These modifications, may alter the structure of the PCNA
trimer and by doing so promote conformational changes that may be
relevant for ordered protein/protein interactions.
[0072] A biological sample can be a body fluid sample, which may
include blood, plasma, lymph, serum, pleural fluid, spinal fluid,
saliva, sputum, urine, semen, tears, synovial fluid or any bodily
fluid that can be tested for the presence of csPCNA isoform.
Alternatively, the biological sample can be a tissue sample,
wherein the cells of the tissue sample may be suspected of being
malignant. For example, tissue sections or cell cultures can be
mounted on glass or plastic slides and contacted with the
antibodies according to standard immunocytochemical protocols.
Tissue extracts or concentrates of cells or cell extracts are also
suitable.
[0073] In another embodiment, a method for diagnosing malignancy is
provided. The method comprises the step of detecting csPCNA in a
biological sample obtained from a person or particularly a patient
suspected of having a malignant condition, wherein the detecting
csPCNA step involves detecting levels of posttranslational
modification involving methylesters disclosed herein.
[0074] In another embodiment, a method to aid in diagnosing
malignancy is provided. The method comprises the step of detecting
posttranslational modifications on csPCNA in malignant cells in a
tissue sample compared to PCNA in normal cells, wherein cells of
the tissue sample are suspected of being malignant, and wherein the
detecting csPCNA step involves detecting methyl esters on csPCNA.
It is to be understood that the malignant cells are not limited to,
malignant cells in tissues such as breast, prostate, blood, brain,
pancreas, smooth or striated muscle, liver, spleen, thymus, lung,
ovary, skin, heart, connective tissue, kidney, bladder, intestine,
stomach, adrenal gland, lymph node, or cervix, or in cell lines,
for example, Hs578T, MCF-7, MDA-MB468, HeLa, HL60, FM3A, BT-474,
MDA-MB-453, T98, LNCaP, LN 99, PC 10, SK-OV-3, MKN-7, KGE 90, KYE
350, or SW 48.
[0075] In another embodiment, a method to aid prognosis of the
development of malignancy is provided. The method involves
detecting csPCNA in a tissue sample by detecting posttranslational
modifications disclosed herein, wherein cells of the tissue sample
may be suspected of being malignant, and correlating the levels of
csPCNA with the progression of a particular malignant disease.
Furthermore, the detection and analysis of posttranslational
modifications on csPCNA can be used to prognose the potential
survival outcome for a patient who has developed a malignancy.
[0076] It is to be understood that the diseases which can be
diagnosed or prognosed using the antibodies include, but are not
limited to, malignancies such as various forms of glioblastoma,
glioma, astrocytoma, meningioma, neuroblastoma, retinoblastoma,
melanoma, colon carcinoma, lung carcinoma, adenocarcinoma, cervical
carcinoma, ovarian carcinoma, bladder carcinoma, lymphoblastoma,
leukemia, osteosarcoma, breast carcinoma, hepatoma, nephroma,
adrenal carcinoma, or prostate carcinoma, esophageal carcinoma. If
a malignant cell expresses csPCNA isoform, the techniques disclosed
herein are capable of detecting the csPCNA isoform.
[0077] Detection techniques involving the detection of
posttranslational modifications disclosed herein, could also detect
malignancy in some of the invasive and non-invasive tumor types in
breast tissue that includes ductal cysts, apocrine metaplasia,
sclerosing adenosis, duct epithelial hyperplasia, non-atypical,
intraductal papillomatosis, columnar cell changes, radial
sclerosing lesion (radial scar), nipple adenoma, intraductal
papilloma, fibroadenoma, lactating papilloma, atypical duct
epithelial hyperplasia, atypical lobular hyperplasia, ductal
carcinoma in situ--sub classified as nuclear grades 1, 2, and 3,
lobular carcinoma-in-situ, pleomorphic lobular carcinoma-in-situ,
intra-mammary lipoma, mammary hamartoma, granular cell tumor,
intramammary fat necrosis, pseudoangiomatous stromal hyperplasia
(PASH), malignant melanoma involving the breast, malignant lymphoma
involving the breast, phyllodes tumor--benign, borderline, and
malignant subclasses, and sarcoma of the breast.
[0078] In another embodiment, methods disclosed herein are used to
determine the malignancy stage in tumors, by comparing levels of
csPCNA in a tumor over time, to follow the progression of a
malignant disease, or a patient's response to treatment. The
methods can also be used to detect malignant cells which have
broken free from a tumor and are present in a patient's
bloodstream, by methods to assay a blood sample for the presence of
the csPCNA isoform. The biological sample can be obtained from
human patients or veterinary patients.
[0079] The term "antibody" includes monoclonal antibodies
(including full length monoclonal antibodies), polyclonal
antibodies, multispecific antibodies (e.g. bispecific antibodies),
and antibody fragments so long as they exhibit the desired
biological activity or specificity.
[0080] Antibodies that specifically recognize posttranslationally
modified nmPCNA or csPCNA can be made.
[0081] The term "modified protein or peptide" refers to the
presence of one or more posttranslational modifications present on
csPCNA or nmPCNA proteins or peptides derived from these proteins.
The term also refers to synthetic and isolated and purified
peptides of csPCNA and nmPCNA that contain one or more
posttranslational modifications. The term also refers to protease
digested peptides of csPCNA and PCNA and peptides of csPCNA and
PCNA fragmented by any known methods that contain one or more
posttranslational modifications.
[0082] All chemicals used herein were obtained from Sigma-Aldrich
(St. Louis, Mo.) or Fisher Scientific (Hampton, N.H.) unless
otherwise stated. Mass spectrometry grade water and acetonitrile
were obtained from Honeywell Burdick and Jackson (Morristown,
N.J.).
[0083] csPCNA and nmPCNA present in samples obtained from
individuals are analyzed for posttranslational modifications using
any standard technique. For example, mass spectrometric analyses is
a suitable technique. Mass spectrometric analysis can be coupled
with other techniques.
[0084] MDA MBA 468 and MCF7 breast cancer cells were obtained from
ATCC and maintained in DMEM (MediaTech, Herndon, Va.) containing
10% FCS (BioWhittaker, Walkersville, Md.) and
Antibiotic-Antimycotic (Invitrogen, Carlsbad, Calif.). Cells were
grown on 100 mm cell culture dishes until 60-70% confluent, rinsed
and scraped with a rubber policeman into ice-cold PBS prior to
pelleting. Cells were fractionated to a nuclear extract as
described in Malkas et al., Biochemistry 1990, 29, 6362-6374.
Briefly, the cells were homogenized using a Dounce.TM. homogenizer
and the nuclei pelleted. Nuclear proteins were subsequently
extracted with 150 mM KCl for 2 h at 4.degree. C. and membranes
pelleted by ultracentrifugation. Nuclear extracts were frozen at
-80.degree. C. until use.
[0085] Isoelectric focusing was performed using an IEF cell and 17
cm pH 4-7 Ready Strip IPG strips (Bio-Rad, Hercules, Calif.).
Protein samples were desalted using Protein Desalting Spin Columns
(Pierce, Rockford, Ill.) and lyophilized in a speed-vac (ATR
Biotech, Laurel, Md.). Lyophilized samples were re-suspended in
rehydration buffer (9 M urea, 4% CHAPS, 0.2% Bio-Lytes (Bio-Rad,
Hercules, Calif.), 2 mM tributylphosphine, 0.001% bromophenol blue)
and passively rehydrated into the IPG strips for 12 h at 20.degree.
C. Isoelectric focusing was carried out following the
manufacturer's instructions (Bio-Rad, Hercules, Calif.). Prior to
SDS-PAGE, the IPG strips were reduced by incubation in buffer (6 M
urea, 0.375 M tris, 2% SDS, 20% glycerol, pH 8.8) containing 20
mg/ml DTT and alkylated in same buffer containing iodoacetamide in
place of DTT. SDS-PAGE was performed on 12% polyacrylamide gels (20
cm.times.20 cm) using a Protean XL apparatus (Bio-Rad, Hercules,
Calif.) with constant current for approximately 5 h. Gels were
fixed with 10% acetic acid/50% methanol in water and stained with
Gel Code Blue (Pierce, Rockford, Ill.) overnight. Imaging was
accomplished using a GS710 Scanning Image Densitometer (Bio-Rad,
Hercules, Calif.) and gel analysis was carried out with Phoretix
Evolution 2D software (NonLinear Dynamics, Inc., Durham, N.C.).
Spot picking was done manually using a 1 mm coring tool (The Gel
Company, San Francisco, Calif.).
[0086] Protein cleavage was performed with trypsin (Promega,
Madison, Wis.), cyanogen bromide (CNBr) (Sigma-Aldrich, St. Louis,
Mo.), GluC, or AspN (Roche, Indianapolis, Ind.) as previously
described with some modification (Rosenfeld et al., Anal Biochem
1992, 203, 173-179; van Montfort et al., Biochim Biophys Acta 2002,
1555, 111-115). Briefly, gel spots were destained in 25 mM ammonium
bicarbonate (ABC)/50% acetonitrile followed by dehydration with
100% acetonitrile and drying in a speed-vac (ATR Biotech, Laurel,
Md.). Spots were then rehydrated in protease solution (20 .mu.g/ml
of either trypsin, GluC, or AspN) in 25 mM ABC. After 10 mM at
4.degree. C., excess protease solution was removed, replaced with
fresh 25 mM ABC, and incubated overnight at 37.degree. C. Peptides
were extracted from the gel by sonication in the presence of 25 mM
ABC/50% acetonitrile (once) and 5% formic acid/50% acetonitrile
(twice). The peptide extracts were pooled and dried in a speed-vac.
Subsequent CNBr cleavages of trypsin digests (on selected samples)
were carried out by re-suspending the dried peptide extracts in 70%
formic acid and adding CNBr to approximately a 200 M excess
relative to the peptide. CNBr cleavage was carried out at room
temperature for 4 h and dried in the speed-vac. All samples were
re-suspended in 1% formic acid immediately prior to analysis.
[0087] Nanoflow HPLC was performed using an IntegraFrit (New
Objective, Inc., Woburn, Mass.) trapping column packed in-house
with Magic C18Aq 5.mu., 200 .ANG. (Michrom, Inc., Auburn, Calif.)
and a 0.05 mm.times.100 mm pulled-tip fused silica column
(PolymicroTechnologies, Phoenix, Ariz.) self-packed with Magic
C18Aq 5.mu., 100 .ANG. material and mounted on a micro-cross held
in place by a custom nanospray stage (Gatlin et al., Anal Biochem
1998, 263, 93-101). Peptides were separated using a 2-50% linear
gradient of acetonitrile containing 0.1% formic acid.
Instrumentation consisted of either a Surveyor HPLC and LCQ
Advantage ion trap mass spectrometer (ThermoElectron, Waltham,
Mass.) or an Ultimate HPLC (LC Packings) and a LCQ DECA XP
(ThermoElectron, Waltham, Mass.). Peak lists were generated from
the raw data using BioWorks 3.1 (ThermoElectron, Waltham, Mass.).
Swissprot database searching was performed using Mascot (Matrix
Science, Inc., Boston, Mass.)(See also, Creasy & Cottrell,
Proteomics 2002, 2, 1426-1434). Parent ion and fragment mass
tolerance of 3 and 0.8 Da, respectively, and up to two missed
cleavage sites were considered. Carbamidomethyl cysteines and
oxidized methionines were selected as variable modifications in a
first pass search of the mammalian database. A subsequent error
tolerant search was performed where trypsin was selected as the
enzyme and glutamate and aspartate methyl esters were additionally
considered as variable modifications.
[0088] While the methods of detecting posttranslational
modification and uses thereof relating to the csPCNA isoform have
been described in detail in the detailed description and in the
Examples below, and with reference to specific embodiments thereof,
it will be apparent to one with ordinary skill in the art that
various changes and modifications can be made therein without
departing from the spirit and scope thereof. All references cited
herein are incorporated by reference in their entirety.
EXAMPLES
[0089] The following examples are provided for the purpose of
exemplification only and are not intended to limit the disclosure
which has been described in broad terms above.
Example 1
Two-Dimensional (2D) Page and Peptide Characterization of csPCNA
Isoform
[0090] A nuclear extract fraction isolated from MDA MB 468 breast
carcinoma cells was resolved by 2D-PAGE (FIG. 1A). Multiple spots
having apparent molecular masses near 36 kDa and pIs at or near 4.5
(PCNA's apparent SDS-PAGE MW and calculated pI) were excised from
the gel and subjected to in-gel digestion with trypsin. The
resulting peptides were analyzed by nanoflow liquid chromatography
(LC) and electrospray tandem mass spectrometry (LC-MS/MS) using a
quadrupole ion trap mass spectrometer. The proteins comprising each
spot were identified by searching the tandem MS data with the
Mascot search engine. Using this approach csPCNA was localized on
2D-PAGE gels. This approach allowed routine identification and
analysis of csPCNA with limited sample handling thus minimizing
potential loss of post-translational modifications. FIG. 1B shows a
representative base peak LC/MS chromatogram of peptides resulting
from the in-gel trypsin digestion of csPCNA excised from 2D-PAGE
gels. In this experiment 25 peptides covering 97% of the
full-length PCNA sequence were identified. A representative csPCNA
peptide identified in this experiment is shown in FIG. 1C. This
peptide eluted at 43.3 min and displayed an m/z of 1038.7 (2+)
(FIG. 1C). Collision induced dissociation (CID) of the peptide
(Roepstorff, P. and Fohlman, J., Biomed Mass Spectrom 1984, 11,
601) revealed the sequence AEDNADTLALVFEAPNQEK (SEQ ID NO: 17),
amino acids 92-110 of human PCNA (FIG. 1D).
Example 2
The Methyl Esterification of csPCNA
[0091] This example demonstrates that csPCNA isoform displays
methyl esterification at one or more amino acid locations. The
LC-MS/MS data identified multiple peptides displaying a 14 Da shift
in parent peptide mass. Interestingly, the identified mass shifts
suggested the presence of a post-translational modification--methyl
esterification. Methylation in mammalian cells is generally
considered an irreversible post-translational modification.
Occurring predominantly on the amine groups of lysine residues and
the N-termini of proteins, methylation has been identified on
proteins such as p53 and histones H3 and H4. However, examination
of the CID spectra for the +14 Da shifted peptides localized the
methyl groups to aspartic and glutamic acid residues consistent
with methyl esterification. FIG. 1E shows the elution of a methyl
esterified peptide (1045.4 m/z [2+]) at 43.8 min in this
experiment. This peptide eluted close to (25 sec after) the
unmodified 1038.7 m/z (2+) peptide (FIG. 1C), which can still be
seen in the MS spectrum. Fragmentation of the 1045.4 m/z ion (FIG.
1F) uncovered a pattern very similar to the 1038.7 m/z peptide
(FIG. 1D). The major difference in these fragmentation spectra are
+14 mass shifts in nearly all of the y-series ions of the 1045.4
m/z peptide compared to the y-series ions of the 1038.7 m/z
peptide. Inspection of the high MW region of the 1045.4 CID
spectrum (FIG. 1F) identifies two b-ions with m/z values of 1943.3
and 1800.2. The 1943.3 ion corresponds to the b.sub.18-ion and
indicates a loss of an unmodified lysine from the C-terminus. This
ion also differs from the b.sub.18-ion (1928.4) observed in the
fragmentation spectrum of the 1038.7 m/z peptide (FIG. 1D) by 14 Da
further suggesting that the lysine is unmodified and the 14-Da mass
shift is on another residue in the peptide. The b.sub.17-ion
(1800.2) in FIG. 1F, on the other hand, closely matches the
b.sub.17-ion (1799.4) in FIG. 1D indicating the loss of a glutamic
acid (129 Da) plus a methyl group (14 Da) or a 143 Da loss between
the b.sub.17 and b.sub.18-ions for the 1045.4 m/z peptide. The
small peaks just to the left of the b.sub.18-ions in FIGS. 1D and
1F have m/z values of 1911.1 and 1925.4, respectively, consistent
with a neutral loss of H.sub.2O or NH.sub.3 from the b.sub.18-ions.
These observations in combination with the shifted y-ion masses
localize the methyl ester to the glutamic acid residue at position
109 in the full-length csPCNA protein.
[0092] In addition to csPCNA, other proteins in the gel were
analyzed for the presence of methyl esterification. Five
representative protein spots are shown in FIG. 1A, and the
identities of these spots and their methyl esterification status
are presented in Table I. Interestingly, one of the five proteins
(Stathmin) analyzed was found to be methyl esterified as well as
N-terminally acetylated. Methyl esterification of csPCNA was not
the result of sample handling (e.g. gel fixation with acetic acid
and methanol), because methyl esterification was observed on only a
small subset of proteins, and consistently on specific csPCNA
residues, instead of its presence throughout all of the proteins
present in the gel.
Example 3
Identification of Methylesterification of csPCNA
[0093] In addition to the AEDNADTLALVFEAPNQEK (SEQ ID NO: 17)
peptide identified in FIG. 1, multiple other csPCNA peptides
consistently displayed 14 Da mass shifts. To successfully identify
all sites of methyl esterification, as well as identify any other
potential post-translational modifications present on the csPCNA
isoform, staggered peptides were generated utilizing different
reagents as shown in sequence maps of the csPCNA isoform. FIG. 2A
shows representative base peak chromatograms of LC-MS/MS
experiments derived from separately digesting csPCNA with trypsin
alone, trypsin followed by cyanogen bromide (CNBr) cleavage, AspN
alone, or GluC alone. These base peak traces show the differences
in the elution profiles for the peptides generated using these
techniques. Digestion with trypsin alone and trypsin and CNBr
provided sequence coverage and the AspN and GluC experiments
provided additional confirmatory data. CNBr cleavage, which cuts
C-terminal to methionine residues, reduced the size of larger
tryptic peptides making those sequences amenable to LC-MS/MS
analysis using the ion trap. This combined digestion was useful in
characterizing the 33-residue tryptic peptide DLINEACWDISSSGVNLQSM
DSSHVSLVQLTLR (SEQ ID NO: 18) (PCNA residues 21-53). Digestion with
AspN and GluC generated confirmatory data although it did not
generate full sequence coverage. This is likely due to multiple
factors. For example, GluC and AspN have a smaller number of
cleavage sites in PCNA as compared to trypsin and therefore
generate larger peptides that are more difficult to analyze.
Additionally, these proteases recognize aspartic and glutamic acid
residues in proteins, the same residues found in this study to be
methyl esterified. Therefore, methyl esterification could
potentially affect protease cleavage producing larger peptides and
ultimately leading to poor sequence coverage. This loss of protease
cleavage can be used as a diagnostic tool to detect methyl
esterification. The peptides generated with a protonated C-terminal
residue like tryptic peptides generally produce good quality CID
spectra. Combined data generated from multiple sequencing
experiments using these different approaches consistently
identified 16 methyl esterified glutamic and aspartic acid residues
on csPCNA from MDA MB 468 and MCF7 breast cancer cells (see Table
III). The resulting sequence maps of csPCNA are presented in FIG.
2B along with any modifications identified by LC-MS/MS. In addition
to methyl esterification, several other modifications were
observed. Oxidized methionines and carbamidomethyl cysteines were
consistently observed on csPCNA and other proteins in all of the
experiments. Additionally, multiple "formylated" serines,
threonines, and tyrosines were observed in the trypsin/CNBr
digests. However, these modifications are likely chemical
modifications that result from sample handling and are not "native"
post-translational modifications.
Example 3A
Identification of Other Posttranslational Modifications on PCNA and
csPCNA
[0094] In addition to identifying methyl esters on csPCNA, the
entire csPCNA molecule was analyzed for the presence of other known
post-translational modifications. In contrast to previous reports
on other forms of PCNA, ubiquitination, sumoylation,
phosphorylation, or acetylation were not identified on csPCNA.
Ubiquitination and sumoylation would lead to a significant mass
shift in PCNA on 2D-PAGE gels, which are not observed with the
csPCNA isoform. Also, no peptides corresponding to either
ubiquitination or sumoylation were identified in any of the
LC-MS/MS experiments of csPCNA, and no csPCNA peptides displayed
mass shifts consistent with ubiquitin or sumoylation conjugation
strongly indicating that csPCNA in the gel spots analyzed here were
neither ubiquitinated nor sumoylated. And although PCNA was
previously reported as phosphorylated, no data supporting the
phosphorylation of any residues of csPCNA was found in these
analyses. None of the csPCNA peptides observed in these analyses
demonstrated a +80 Da mass shift and/or a neutral loss if
H.sub.3PO4 (98 Da), which is consistent with reports showing that
PCNA is acetylated and not phosphorylated. Additionally, the gels
were immunoblotted for the presence phosphoserine,
phosphothreonine, phosphotyrosine, acetylated lysine, as well as
poly (ADP) ribose and were unable to detect these
post-translational modifications on PCNA.
[0095] The csPCNA isoform in breast cancer cells is not
phosphorylated, acetylated, ubiquitinated, or sumoylated, but is
instead methyl esterified. Similar to acetylation and
phosphorylation, methyl esterification could change its migration
on 2D-PAGE. However, unlike acetylation and phosphorylation, which
would shift the molecule to a more acidic pI, methyl esterification
would cause the protein to resolve at a more basic pI. It could
therefore be postulated that the low abundance acidic isoform seen
in FIG. 1A (white arrow) may be an isoform that contains fewer or
no methyl esters as compared to the csPCNA isoform.
[0096] The csPCNA isoform contains a low amount of methyl
esterification compared to the normal or non-malignant form of PCNA
(nmPCNA or simply PCNA). The non-malignant or basic PCNA isoform
likely contains a higher level of methyl esterification. This
conclusion is based, in part, on the fact that methyl
esterification modifies acidic residues and would shift the protein
to a more basic pI (due to loss of acidic charge) and the csPCNA
isoform is very close to its calculated pI of 4.5. However,
acetylation, phosphorylation and ADP-ribosylation would shift a
protein to a more acidic pI below 4.5 (due to addition of an acidic
charge). Therefore, these modifications are not likely responsible
for the pI shift. Measuring the extent of methyl esterification on
PCNA and csPCNA determines malignant from non-malignant (csPCNA
from nmPCNA). Using the methods disclosed herein, the
methylesterification levels of csPCNA and nmPCNA are determined and
compared for diagnosis of malignancy. For example, Table II
provides methylesterification state of various csPCNA-derived
peptides and the % modified in a heterogeneous population. Table II
can be used as a comparison chart for determining the various
methylesterification levels in diagnosing malignancy.
Example 4
Semi-Quantitation of Methyl Esterified csPCNA Peptides
[0097] The identification of methyl esters on csPCNA with respect
to the pI of the isoform was further investigated. PCNA has a
calculated pI of approximately 4.5 and the pI of csPCNA, as
determined after calibration of the 2D-PAGE gel using the pIs of
surrounding proteins, was slightly higher, approximately 4.6. In
contrast, if 100% of all 16 acidic residues identified in FIG. 2
were methyl esterified, the protein's pI would likely shift basic
more dramatically than 0.1 pH units (e.g., 5.66). There may be
additional residues that are modified to produce the basic or
nmPCNA isoform. The nmPCNA isoform may also be methyl esterified on
different and/or additional residues than csPCNA. The methods
discloses herein enable one of ordinary skill in the art to
determine methylesterification levels of csPCNA and nmPCNA. The
relative abundances of the methyl esterified peptides was measured
and compared to the unmodified peptides. This was accomplished by
measuring and comparing the peak areas of each unmodified peptide
and its methyl esterified counterpart. Comparison of the peak areas
revealed a relative abundance for each methyl ester identified in
this LC-MS/MS experiment as shown in Table II. Each of the peptides
show only partial methyl esterification (<25%) when the peak
areas are compared. Therefore the csPCNA isoform is likely to be
comprised of a heterogeneous population of PCNA molecules with the
same pI. In other words, a single csPCNA molecule likely exhibits
one or few methyl esters, but not 16. But the one or few methyl
esters can occur on 16 different residues throughout the protein.
This heterogeneity of csPCNA is illustrated by the presence of
methyl esterification on the C-terminal peptide of csPCNA. The
unmodified peptide, IEDEEGS (SEQ ID NO: 16) (778 m/z), eluted at
28.9 min (FIG. 3A) and the CID spectrum of this peptide is
consistent with a peptide containing unmodified acidic residues
(FIG. 3B). Interestingly, in the selected ion chromatogram for
methyl esterified species (792 m/z) of this peptide, two peaks are
identified with 2-3 min increased retention times. This is likely
due to an increased hydrophobic character and loss of charge
imparted by methyl esterification. The resolution of these two
peaks was therefore indicative of a difference in structure of
these peptides. Inspection of the CID spectra identifies that the
peptides are methyl esterified but on different residues (FIGS. 3C
and D). Because no peptides harboring methyl esters on both
residues were observed, the appearance of these peptides most
likely resulted from the analysis of a heterogeneous population of
csPCNA.
[0098] It is possible that the observed heterogeneity and low
percentage of modified species could be the result of the facile
lability of the methyl ester modifications themselves. Some reports
indicate that protein methyl esterification modifications were
short lived in neutral and basic solutions. Therefore, protein
methyl esters, like those found on csPCNA, can spontaneously
hydrolyze leaving an unmodified residue and methanol. Additionally,
the basic and oxidizing conditions of SDS-PAGE can also lead to
loss of methyl esters from PCNA, and attempts to resolve the basic
PCNA isoform, a highly methyl esterified form of PCNA, to its basic
pI appears to display a spontaneous regression towards a more
acidic pI (FIG. 4).
[0099] A high level of methyl esters likely cause PCNA to focus to
a basic pI as shown in the immunoblot in FIG. 4 (approximately pH
8.8-9.0). However, focusing of this isoform may not be uniform
(streaky) and may be present at a lower intensity. The basic pHs at
which this isoform resolves may not be conducive to maintain all of
the methyl esterification on the protein. The inability to focus at
a specific pI observed on this gel (FIG. 4) is likely due to the
concomitant loss of one or more of the methyl esters due to the
focusing at a basic pH. Spontaneous hydrolysis of the methyl esters
occur, liberating methanol and an unmodified amino acid side chain.
Regeneration of the acidic side chains by this "basic hydrolysis"
likely causes PCNA's pI to shift from a basic one to a more acidic
one, as evidenced by the accumulation of PCNA towards the mores
acidic side of the gel (pH 7).
[0100] Identification and analysis of methylesterification can be
performed under conditions that minimize loss of methylesters. For
example, a method describing acidic 2D-PAGE that uses conditions
able to preserve protein methyl esters has been described (O'Connor
et al., Anal Biochem 1985, 148, 79-86). However, many of the
available proteases that recognize PCNA are active in neutral to
basic pHs and it is possible that some significant amount of methyl
esterification would be lost during the digestion.
[0101] In the intact cell or in extracts, the enzyme(s) responsible
for the methyl esterification may be active and can modify residues
that have lost methyl esters to spontaneous hydrolysis. Separation
of PCNA from the enzyme(s) responsible for the methyl
esterification and incubation in conditions supporting hydrolysis
(e.g., pH above 7.0) may lead to loss of one or more methyl esters.
For example, such loss of methyl esters can be minimized by
maintaining a slightly acidic condition during sample handling and
analysis.
TABLE-US-00001 TABLE I Analysis of methylesterification status of
various proteins. Molecular Methyl Swissprot weight Peptides
Esterified Sequence Spot.sup.a Protein Accession (M.sub.r) pI
Identified Peptides.sup.b coverage.sup.c i Ezrin P15311 69,225 5.95
16 0 32% ii Stathmin P16949 17,161 5.77 16 7 62% iii Calreticulin
P27797 48,112 4.29 7 0 33% precursor iv Inorganic Q15181 32,639
5.54 20 0 75% pyrophosphatase v Translationally P13693 19583 4.84 8
0 70% controlled tumor protein .sup.aThe locations of the protein
spots are identified in FIG. 1A. .sup.bPeptides clearly
demonstrating + 14 mass shift on either aspartic or glutamic acid
residues. .sup.cSequence coverage is calculated by dividing the
number of amino acid residues identified by the total number of
residues in the protein.
TABLE-US-00002 TABLE II Methylesterification state of various
csPCNA-derived peptides. Methyl SEQ Observed Charge Calc. Peak
Ester Peptide Sequence.sup.a ID NO: m/z State mass Area (%).sup.b
Score.sup.c M.sub.oFE.sub.mAR 19 343.37 2 682.31 5.9 .times.
10.sup.6 3.6 19 IE.sub.mDEEGS 2 792.30 1 791.32 2.8 .times.
10.sup.7 7.3 27 IEDEE.sub.mGS 3 792.47 1 791.32 2.7 .times.
10.sup.7 7.0 25 VSDYE.sub.mM.sub.oK 20 451.9 2 900.39 8.1 .times.
10.sup.6 11.4 46 M.sub.oPSGE.sub.mFAR 21 463.20 2 923.42 1.4
.times. 10.sup.7 2.5 50 LSQTSNVD.sub.mK 6 503.96 2 1004.51 1.5
.times. 10.sup.6 21.1 40 C.sub.caAGNE.sub.mDIITLR 22 639.44 2
1274.63 1.7 .times. 10.sup.7 8.8 66 FSASGE.sub.mLGNGNIK 8 655.11 2
1306.65 7.6 .times. 10.sup.7 2.7 99 AEDNADTLALVFEAPNQE.sub.mK 9
1045.93 2 2088.00 5.0 .times. 10.sup.7 3.5 97
AE.sub.mDNADTLALVFEAPNQEK 10 1046.01 2 2088.00 2.0 .times. 10.sup.7
3.9 89 AED.sub.mNADTLALVFEAPNQEK 11 1045.31 2 2088.00 4.1 .times.
10.sup.7 12.7 102 AEDNADTLALVFE.sub.mAPNQEK 12 1045.69 2 2088.00
3.4 .times. 10.sup.7 4.5 94
LM.sub.oD.sub.mLDVEQLGIPEQEYSC.sub.caVVK 23 1249.50 2 2494.20 9.5
.times. 10.sup.7 10.3 78 ATPLSSTVTLSM.sub.oSADVPLVVE.sub.mYK 24
1220.83 2 2437.27 1.35 .times. 10.sup.7 8.3 95
LSQTSNVDKEEEAVTIEM.sub.oNE.sub.mPVQ 25 1108.28 3 3320.64 3.43
.times. 10.sup.9d 8.7 50 LTFALR .sup.aPeptide modifications
presented are oxidized methionine (M.sub.o), carbamidomethyl
cysteine (C.sub.ca), methyl esterified glutamic acid (E.sub.m), and
methyl esterified aspartic acid (D.sub.m). .sup.bPercent methyl
ester was calculated by dividing the peak areas of the methyl
esterified peptides by the combined peak areas for the methyl
esterified and unmodified peptides. .sup.cMascot scores are
reported as -10log(P), where P is the probability that the match is
a random event. .sup.dData generated using an LCQ DECA XP compared
to an LCQ Advantage.
TABLE-US-00003 TABLE III Amino acid positions of methylesters on
csPCNA Position Methyl Ester Residue (1-261 a.a.) 1 Glutamic acid 3
2 Glutamic acid 85 3 Glutamic acid 93 4 Aspartic acid 94 5 Glutamic
acid 104 6 Glutamic acid 109 7 Glutamic acid 115 8 Aspartic acid
120 9 Glutamic acid 132 10 Glutamic acid 143 11 Glutamic acid 174
12 Aspartic acid 189 13 Glutamic acid 201 14 Glutamic acid 238 15
Glutamic acid 256 16 Glutamic acid 259
Sequence CWU 1
1
3115PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 1Met Phe Glu Ala Arg1 527PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 2Ile
Glu Asp Glu Glu Gly Ser1 537PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptide 3Ile Glu Asp Glu Glu Gly Ser1
547PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 4Val Ser Asp Tyr Glu Met Lys1 558PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 5Met
Pro Ser Gly Glu Phe Ala Arg1 569PRTArtificial SequenceDescription
of Artificial Sequence Synthetic peptide 6Leu Ser Gln Thr Ser Asn
Val Asp Lys1 5711PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 7Cys Ala Gly Asn Glu Asp Ile Ile Thr Leu
Arg1 5 10813PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 8Phe Ser Ala Ser Gly Glu Leu Gly Asn Gly
Asn Ile Lys1 5 10919PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 9Ala Glu Asp Asn Ala Asp Thr Leu Ala Leu
Val Phe Glu Ala Pro Asn1 5 10 15Gln Glu Lys1019PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 10Ala
Glu Asp Asn Ala Asp Thr Leu Ala Leu Val Phe Glu Ala Pro Asn1 5 10
15Gln Glu Lys1119PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 11Ala Glu Asp Asn Ala Asp Thr Leu Ala
Leu Val Phe Glu Ala Pro Asn1 5 10 15Gln Glu Lys1219PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 12Ala
Glu Asp Asn Ala Asp Thr Leu Ala Leu Val Phe Glu Ala Pro Asn1 5 10
15Gln Glu Lys1321PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 13Leu Met Asp Leu Asp Val Glu Gln Leu
Gly Ile Pro Glu Gln Glu Tyr1 5 10 15Ser Cys Val Val Lys
201423PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 14Ala Thr Pro Leu Ser Ser Thr Val Thr Leu Ser Met
Ser Ala Asp Val1 5 10 15Pro Leu Val Val Glu Tyr Lys
201529PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 15Leu Ser Gln Thr Ser Asn Val Asp Lys Glu Glu Glu
Ala Val Thr Ile1 5 10 15Glu Met Asn Glu Pro Val Gln Leu Thr Phe Ala
Leu Arg 20 25167PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 16Ile Glu Asp Glu Glu Gly Ser1
51719PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 17Ala Glu Asp Asn Ala Asp Thr Leu Ala Leu Val Phe
Glu Ala Pro Asn1 5 10 15Gln Glu Lys1833PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 18Asp
Leu Ile Asn Glu Ala Cys Trp Asp Ile Ser Ser Ser Gly Val Asn1 5 10
15Leu Gln Ser Met Asp Ser Ser His Val Ser Leu Val Gln Leu Thr Leu
20 25 30Arg195PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 19Met Phe Glu Ala Arg1 5207PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 20Val
Ser Asp Tyr Glu Met Lys1 5218PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptide 21Met Pro Ser Gly Glu Phe Ala
Arg1 52211PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 22Cys Ala Gly Asn Glu Asp Ile Ile Thr Leu Arg1 5
102321PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 23Leu Met Asp Leu Asp Val Glu Gln Leu Gly Ile Pro
Glu Gln Glu Tyr1 5 10 15Ser Cys Val Val Lys 202423PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 24Ala
Thr Pro Leu Ser Ser Thr Val Thr Leu Ser Met Ser Ala Asp Val1 5 10
15Pro Leu Val Val Glu Tyr Lys 202529PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 25Leu
Ser Gln Thr Ser Asn Val Asp Lys Glu Glu Glu Ala Val Thr Ile1 5 10
15Glu Met Asn Glu Pro Val Gln Leu Thr Phe Ala Leu Arg 20
2526261PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 26Met Phe Glu Ala Arg Leu Val Gln Gly Ser Ile Leu
Lys Lys Val Leu1 5 10 15Glu Ala Leu Lys Asp Leu Ile Asn Glu Ala Cys
Trp Asp Ile Ser Ser 20 25 30Ser Gly Val Asn Leu Gln Ser Met Asp Ser
Ser His Val Ser Leu Val 35 40 45Gln Leu Thr Leu Arg Ser Glu Gly Phe
Asp Thr Tyr Arg Cys Asp Arg 50 55 60Asn Leu Ala Met Gly Val Asn Leu
Thr Ser Met Ser Lys Ile Leu Lys65 70 75 80Cys Ala Gly Asn Glu Asp
Ile Ile Thr Leu Arg Ala Glu Asp Asn Ala 85 90 95Asp Thr Leu Ala Leu
Val Phe Glu Ala Pro Asn Gln Glu Lys Val Ser 100 105 110Asp Tyr Glu
Met Lys Leu Met Asp Leu Asp Val Glu Gln Leu Gly Ile 115 120 125Pro
Glu Gln Glu Tyr Ser Cys Val Val Lys Met Pro Ser Gly Glu Phe 130 135
140Ala Arg Ile Cys Arg Asp Leu Ser His Ile Gly Asp Ala Val Val
Ile145 150 155 160Ser Cys Ala Lys Asp Gly Val Lys Phe Ser Ala Ser
Gly Glu Leu Gly 165 170 175Asn Gly Asn Ile Lys Leu Ser Gln Thr Ser
Asn Val Asp Lys Glu Glu 180 185 190Glu Ala Val Thr Ile Glu Met Asn
Glu Pro Val Gln Leu Thr Phe Ala 195 200 205Leu Arg Tyr Leu Asn Phe
Phe Thr Lys Ala Thr Pro Leu Ser Ser Thr 210 215 220Val Thr Leu Ser
Met Ser Ala Asp Val Pro Leu Val Val Glu Tyr Lys225 230 235 240Ile
Ala Asp Met Gly His Leu Lys Tyr Tyr Leu Ala Pro Lys Ile Glu 245 250
255Asp Glu Glu Gly Ser 26027261PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptide 27Met Phe Glu Ala Arg Leu Val
Gln Gly Ser Ile Leu Lys Lys Val Leu1 5 10 15Glu Ala Leu Lys Asp Leu
Ile Asn Glu Ala Cys Trp Asp Ile Ser Ser 20 25 30Ser Gly Val Asn Leu
Gln Ser Met Asp Ser Ser His Val Ser Leu Val 35 40 45Gln Leu Thr Leu
Arg Ser Glu Gly Phe Asp Thr Tyr Arg Cys Asp Arg 50 55 60Asn Leu Ala
Met Gly Val Asn Leu Thr Ser Met Ser Lys Ile Leu Lys65 70 75 80Cys
Ala Gly Asn Glu Asp Ile Ile Thr Leu Arg Ala Glu Asp Asn Ala 85 90
95Asp Thr Leu Ala Leu Val Phe Glu Ala Pro Asn Gln Glu Lys Val Ser
100 105 110Asp Tyr Glu Met Lys Leu Met Asp Leu Asp Val Glu Gln Leu
Gly Ile 115 120 125Pro Glu Gln Glu Tyr Ser Cys Val Val Lys Met Pro
Ser Gly Glu Phe 130 135 140Ala Arg Ile Cys Arg Asp Leu Ser His Ile
Gly Asp Ala Val Val Ile145 150 155 160Ser Cys Ala Lys Asp Gly Val
Lys Phe Ser Ala Ser Gly Glu Leu Gly 165 170 175Asn Gly Asn Ile Lys
Leu Ser Gln Thr Ser Asn Val Asp Lys Glu Glu 180 185 190Glu Ala Val
Thr Ile Glu Met Asn Glu Pro Val Gln Leu Thr Phe Ala 195 200 205Leu
Arg Tyr Leu Asn Phe Phe Thr Lys Ala Thr Pro Leu Ser Ser Thr 210 215
220Val Thr Leu Ser Met Ser Ala Asp Val Pro Leu Val Val Glu Tyr
Lys225 230 235 240Ile Ala Asp Met Gly His Leu Lys Tyr Tyr Leu Ala
Pro Lys Ile Glu 245 250 255Asp Glu Glu Gly Ser
26028141PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 28Ala Leu Lys Asp Leu Ile Asn Glu Ala Cys Trp Asp
Ile Ser Ser Ser1 5 10 15Gly Val Asn Leu Gln Ser Met Asp Ser Ser His
Val Ser Leu Val Gln 20 25 30Leu Thr Leu Arg Ser Glu Ala Pro Asn Gln
Glu Lys Val Ser Asp Tyr 35 40 45Glu Met Lys Leu Met Asp Leu Asp Val
Glu Gln Leu Gly Ile Pro Glu 50 55 60Gln Glu Tyr Ser Cys Val Val Lys
Met Pro Ser Gly Glu Leu Gly Asn65 70 75 80Gly Asn Ile Lys Leu Ser
Gln Thr Ser Asn Val Asp Lys Glu Glu Glu 85 90 95Ala Val Thr Ile Glu
Met Asn Glu Pro Val Gln Leu Thr Phe Ala Leu 100 105 110Arg Tyr Leu
Asn Phe Phe Thr Lys Ala Thr Pro Leu Ser Ser Thr Val 115 120 125Thr
Leu Ser Met Ser Ala Asp Val Pro Leu Val Val Glu 130 135
14029154PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 29Asp Leu Ile Asn Glu Ala Cys Trp Asp Ile Ser Ser
Ser Gly Val Asn1 5 10 15Leu Gln Ser Met Asp Ser Ser His Val Ser Leu
Val Gln Leu Thr Leu 20 25 30Arg Ser Glu Gly Phe Asp Arg Asn Leu Ala
Met Gly Val Asn Leu Thr 35 40 45Ser Met Ser Lys Ile Leu Lys Cys Ala
Gly Asn Glu Asp Ile Ile Thr 50 55 60Leu Arg Ala Glu Asp Asn Ala Asp
Thr Leu Ala Leu Val Phe Glu Ala65 70 75 80Pro Asn Gln Glu Lys Val
Ser Asp Tyr Glu Met Lys Leu Met Asp Leu 85 90 95Ser His Ile Gly Asp
Gly Val Lys Phe Ser Ala Ser Gly Glu Leu Gly 100 105 110Asn Gly Asn
Ile Lys Leu Ser Gln Thr Ser Asn Val Asp Val Pro Leu 115 120 125Val
Val Glu Tyr Lys Ile Ala Asp Met Gly His Leu Lys Tyr Tyr Leu 130 135
140Ala Pro Lys Ile Glu Asp Glu Glu Gly Ser145 15030261PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 30Met
Phe Glu Ala Arg Leu Val Gln Gly Ser Ile Leu Lys Lys Val Leu1 5 10
15Glu Ala Leu Lys Asp Leu Ile Asn Glu Ala Cys Trp Asp Ile Ser Ser
20 25 30Ser Gly Val Asn Leu Gln Ser Met Asp Ser Ser His Val Ser Leu
Val 35 40 45Gln Leu Thr Leu Arg Ser Glu Gly Phe Asp Thr Tyr Arg Cys
Asp Arg 50 55 60Asn Leu Ala Met Gly Val Asn Leu Thr Ser Met Ser Lys
Ile Leu Lys65 70 75 80Cys Ala Gly Asn Glu Asp Ile Ile Thr Leu Arg
Ala Glu Asp Asn Ala 85 90 95Asp Thr Leu Ala Leu Val Phe Glu Ala Pro
Asn Gln Glu Lys Val Ser 100 105 110Asp Tyr Glu Met Lys Leu Met Asp
Leu Asp Val Glu Gln Leu Gly Ile 115 120 125Pro Glu Gln Glu Tyr Ser
Cys Val Val Lys Met Pro Ser Gly Glu Phe 130 135 140Ala Arg Ile Cys
Arg Asp Leu Ser His Ile Gly Asp Ala Val Val Ile145 150 155 160Ser
Cys Ala Lys Asp Gly Val Lys Phe Ser Ala Ser Gly Glu Leu Gly 165 170
175Asn Gly Asn Ile Lys Leu Ser Gln Thr Ser Asn Val Asp Lys Glu Glu
180 185 190Glu Ala Val Thr Ile Glu Met Asn Glu Pro Val Gln Leu Thr
Phe Ala 195 200 205Leu Arg Tyr Leu Asn Phe Phe Thr Lys Ala Thr Pro
Leu Ser Ser Thr 210 215 220Val Thr Leu Ser Met Ser Ala Asp Val Pro
Leu Val Val Glu Tyr Lys225 230 235 240Ile Ala Asp Met Gly His Leu
Lys Tyr Tyr Leu Ala Pro Lys Ile Glu 245 250 255Asp Glu Glu Gly Ser
2603121PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 31Leu Met Asp Leu Asp Val Glu Gln Leu Gly Ile Pro
Glu Gln Glu Tyr1 5 10 15Ser Cys Val Val Lys 20
* * * * *