ACPA-NEGATIVE RA DIAGNOSTIC MARKER AND APPLICATION THEREOF

TECHNICAL FIELD

The present invention belongs to biological detection field, in particular, relates to a kind of ACPA-negative RA diagnostic marker and application thereof.

BACKGROUND ART

Rheumatoid arthritis (RA) is a chronic autoimmune disease, mainly characterized by the multiple joint inflammation and local bone destruction. In developing countries, rheumatoid arthritis affects nearly 0.5% to 1% of the population. In general, the incidence of RA in women is higher than that in men, and the elderly are more likely to develop RA than the youth. The clinical manifestations of rheumatoid arthritis display heterogeneity, ranging from self-limiting disease with mild symptoms to fast developed inflammation along with joint destruction and severe physical disability. Due to differences in disease performance, classification criteria were developed as the basis for disease definition, selection of standardized clinical trials, and comparison of multicenter studies. In 1987, the classification criteria for RA was established by the American College of Rheumatology (ACR). However, too strict definition for arthritis in the classification criteria leads to a low sensitivity to RA diagnosis in practice, a large number of early RA patients failed to be identified. It is of vital importance that new-onset RA case can benefit from early effective intervention, avoiding progression to chronic and erosive RA or even disability, thus affecting long-term quality of life and increasing disease mortality. Therefore, early diagnosis and treatment serve as the key to preventing irreversible joint destruction. In 2009, the ACR/EULAR standard for RA was updated with higher sensitivity to diagnose and treat RA early, but the specificity still needs improving.

Anti citrulline polypeptide antibody (ACPAs) positivity is included in the 2009 ACR revised criteria. ACPA is regarded as the serum specific biomarker of RA, the emergence of which improves our understanding of the pathogenesis of RA. But the exact cause of RA is still unknown until now. Environmental and genetic factors are acknowledged as the “trigger” of clinical symptoms in RA. Moreover, there are still a number of ACPA-negative RA patients in clinical practice, and thanks to the researchers' more understanding of the disease, they gradually realize that there is a certain clinical heterogeneity in ACPA-positive RA patients and ACPA-negative RA patients. The lack of specific biomarkers for ACPA-negative RA patients makes it quite difficult to provide accurate diagnosis and treatment.

Autoantibodies have been found in the serum of RA patients for more than 70 years. The rheumatoid factor, targeting the Fc fragment of human IgG, is the first group of autoantibodies identified, including various isotypes such as IgG and IgM. But RF is not the antibody specific to RA since RF can also be detected in many other conditions including the normal elderly, patients with other autoimmune diseases and 15% of healthy individuals. In the years 1964 and 1979, other antibodies, i.e. anti-perinuclear factor antibodies (APF) and anti-keratin antibodies (AKA) were found in RA patients respectively. Although these two antibodies have high specificity in the diagnosis of RA, they are difficult to be detected. RF is still applied for the diagnosis of RA and therefore included in the 1987 ACR RA criteria. Until the year 1995, studies revealed that APF and AKA were similar autoantibodies, both targeting citrulline residue formed by the deimidization of arginine residues. In the year 2002, the first commercialized kit to detect ACPA was developed, enabling ACPA to serve as conventional biomarker for RA. The study of this autoantibody system has deepened our understanding and improved the classification of RA. Therefore, both RF and ACPA have become parts of ACR/EULAR2010 classification criteria.

Recently, it's reported that a novel autoantibody subtype recognizing carbamylated proteins (anti-CarP) was identified in RA patient serum. The autoantibody system is independent of ACPA, since autoantibodies of RA are able to distinguish citrullinated and carbamylated antigens. Correspondingly, anti-CarP antibodies are detected in a part of ACPA-negative patients. In the last few years, the identification of autoantibodies targeting citrullinated and carbamylated proteins helps understand the pathogenesis and etiology of RA. Both carbamylation and citrullination are post-translational modifications, making proteins be carbamylated or citrullinated respectively and replacing positively charged amino acids with the neutral ones. Citrullinated proteins are derived from PAD while Carbamylated proteins are obtained by converting the lysine to homocitrulline by chemical reaction. Citrulline and homocitrulline are chemically similar but located at different sites of the protein because of different location of arginine and lysine. And the homocitrulline has one more formyl group compared to the citrulline. Although there're antibodies reactive to both structures, some anti-CarP antibodies do not respond to citrulline, while some anti-citrulline antibodies also fail to react to CarP.

In 2009, Auger et al. tested serum samples of ACPA-negative RA patients with chips containing 8268 proteins and identified PAD4 and BRAF as candidate biomarkers. Anti-PAD antibodies targeting enzymes involving protein citrullination, attracted extensive attention, since it is found that these antibodies can not only bind to targets, but also activate PAD. Anti-PAD antibodies increase the catalytic capacity of PAD4 by decreasing the calcium requirement of this citrullinated enzyme. Charpin C et al. found that there are antibodies against the BRAF catalytic domain in sera from patients with RA, which are mainly focused on amino acids 416 to 766 and the antibodies are present in 30% of ACPA-negative RA patients. Meantime, 33% of patients who are anti-BRAF antibodies positive are ACPA negative. In addition, anti-BRAF antibodies can be found in 4% of AS patients and 6% of healthy controls.

As mentioned above, RA is a chronic autoimmune disease, for which autoantibodies marker detection matters a lot. RA is characterized by clinical heterogeneity. Some patients' symptoms are self-limiting and mild, while some suffer from rapidly progressive inflammation, joint destruction and severe disability. The heterogeneity of RA clinical manifestations leads to great differences of reactions to treatment. For now, there's no way to predict the effect of specific treatment for the lack of efficient biomarkers to sub-classify RA patients. The identification of ACPA is of vital importance since it is the first time to classify RA patients with serum marker. However, ACPA-positive and ACPA-negative RA patients appear to be quite different in genetics of disease and environmental determinants, molecular features of the joint involvement, remission rate and response to therapies. Many ACPA-negative RA patients have limited targets to subclassify, because the lack of potent biomarkers leads to limited targets to classify the clinical manifestation of RA. Identifying more autoantibodies especially for ACPA-negative antibodies can contribute to unraveling the pathogenic role of autoantibodies and the pathogenesis of RA.

In developing countries including China, the incidence and disability rate of RA stay high, making it important to diagnose early and correctly. Identifying more for ACPA-negative RA related autoantibody markers and autoantigens predicting disease activity or therapeutic efficacy, is indispensable to reduce the disability rate of RA.

SUMMARY OF THE INVENTION

To solve the problems mentioned above, the present invention provides an ACPA-negative RA diagnostic marker and application thereof.

The ACPA-negative RA diagnostic marker of the present invention includes DOHH (Deoxyhypusine dioxygenase), PAGE5 (P antigen family member 5), DUSP11 (Dual specificity protein phosphatase 11) and PTX3 (Pentraxin-related protein 3).

The present invention also provides use of DOHH, PAGE5, DUSP11, PTX3 and their fragments in preparation of reagents for the diagnosis of ACPA-negative RA.

wherein, the diagnosis includes detecting the level of the antibody reactive to DOHH, PAGE5, DUSP11, PTX3 or their fragments in ACPA-negative RA patient biological samples, optionally Compare the level of the antibody with controls, wherein, the detectable increase of the antibody reactive to DOHH, PAGE5, DUSP11, PTX3 indicates the possibility of developing ACPA-negative RA.

wherein, the biological sample refers to serum sample.

wherein, the antibody level of the DOHH, PAGE5, DUSP11, or PTX3 is detected by procedures below, including:

a making biological samples from patients contact with DOHH, PAGE5, DUSP11, PTX3 and their fragments;

b making the antibodies in the biological sample and DOHH, PAGE5, DUSP11, PTX3 or their fragments to form an antibody-protein complex;

c. washing to remove any antibodies uncombined;

d. adding labeled antibodies reactive to antibodies from the biological sample;

e. washing to remove labeled detection antibodies that are uncombined; and

f. transforming the marker of the detection antibodies into detectable signal; wherein the presence of detectable signal indicates the presence of anti-DOHH, anti-PAGE5, anti-DUSP11 or anti-PTX3 antibodies in patients.

wherein, DOHH, PAGE5, DUSP11, PTX3 or their fragments are deposited or fixed in solid phase support.

wherein, the solid support refers to forms of latex beads, porous flat plate or membranes.

wherein, the detection antibodies are labeled by markers that are covalently linked to the enzyme and have fluorescent compounds or metal, or chemiluminescent compounds.

The present invention also provides a device to identify the presence or expression level of antibodies in patients' samples, which are reactive to DOHH, PAGE5, DUSP11, PTX3 or their fragments or combinations, including

a. at least one of DOHH, PAGE5, DUSP11, PTX3 or their fragments, or their combinations; and

b. at least one kind of solid phase support, wherein the DOHH, PAGE5, DUSP11, PTX3 or their fragments, or combinations are deposited in the support mentioned;

The device in the present invention further includes the detection antibodies, wherein the detection antibodies specifically combine with the antibodies in patients' sample that are reactive to DOHH, PAGE5, DUSP11, PTX3 and their fragments or combination, and the detection antibodies can produce detectable signal.

wherein the sample of patients refers to serum sample.

By hybridizing the high density protein chip with RA serum, the present invention identified 35 candidate ACPA-negative RA autoantigens with the specificity more than 90% and the sensitivity more than 25%, and 7 candidate autoantigens associated with prediction of the disease activity and 6 candidate autoantigens associated with prediction of therapy efficacy (two candidate autoantigens are included in the analysis of different groups). To validate the sensitivity and specificity of these autoantigens, a protein chip containing 46 candidate RA autoantigens was constructed. A large number of serum samples (including serum from 9 OA, 38 SLE, 39 AS, 18 BD, 10 ANCA, 21SS, 102 healthy controls and 290 RA) are hybridized with autoantigen chip. Data shows that 4 proteins are newly-identified antigens with high sensitivity and specificity: DOHH, DUSP11, PTX3, PAGE5, and the sensitivity of DOHH and PTX3 as diagnostic markers are 49.66% and 43.54% respectively. In the 7 candidate autoantigens related to prediction of the disease activity, autoantigen RRN3 can distinguish moderate to low activity and high activity in RA successfully and its AUC reaches 0.65. RRN3 and PLEKHG2 can distinguish moderate to low activity and high activity in ACPA-positive RA successfully: the AUC are 0.845 and 0.817, respectively. In 6 candidate autoantigens to predict therapeutic efficacy, ERH can predict the therapeutic efficacy, with the AUC of 0.733.

DESCRIPTION OF DRAWINGS

FIG. 1: Quality control of protein chips.

FIG. 2: The correlation of all recombinant protein probe parallel points on the protein chips by GST.

FIG. 3: Partial images formed by hybridizing high-density protein chip with small number of serum samples.

FIG. 4: Signal value distribution of Blank and EMPTY on protein chips.

FIG. 5: Signal value distribution of PTX3 in RA patients, healthy and diseases control groups.

FIG. 6: Signal value distribution of RRN3 in different disease activity group.

FIG. 7: Signal value distribution of two antigens in ACPA-positive RA with different disease activity.

FIG. 8: Signal value distribution of ERH in RA group with different efficacy and the AUC curve.

DETAILED DESCRIPTION OF EMBODIMENTS

The following examples are described to illustrate the present invention, but not limit the scope of the present invention.

Serum samples (all samples were collected and clinically tested at department of rheumatology, Peking Union Medical College Hospital)

The study used 647 serum samples including:

350 samples from RA patients, age (mean±SD): 45.2±12.5

9 samples from osteoarthritis(OA) patients, age (mean±SD): 67.2±16.6

48 samples from systemic lupus erythematosus(SLE) patients, age (mean±SD): 36.8±12.4

28 samples from Behcet's disease (BD) patients, age (mean±SD): 54.2±20.7

10 samples from antineutrophil cytoplasmic antibody-associated vasculitis patients, age (mean±SD): 46.9±16.3

39 samples from ankylosing-spondylitis(AS) patients, age (mean±SD): 38.2±15.1

21 samples from Sjogren Syndrome(SS) patients, age (mean±SD): 52.7±13.2

10 samples from Takayasu arteritis(TA) patients, age (mean±SD): 38.4±13.5

132 samples from healthy controls, age (mean±SD): 37.5±12.1

RA was diagnosed according to the 2010 ACR/EULAR criteria for RA, and OA, SLE, BD, ANCA, AS, SS and TA were diagnosed according to corresponding diagnosis and/or criteria.

All serum samples were collected at Peking Union Medical College Hospital during a period from 2006 to 2014. All serum samples are from patients confirm diagnosis at clinic and for those with controversial diagnoses, three chief physicians were invited to identify the final diagnosis.

All RA serum samples were tested for corresponding antibodies, including three ANAs: ANA-IF (immunofluorescence method), DNA-IF (immunofluorescence method), ds-DNA(ELISA), anti-CCP antibodies, i.e. ACPA (positive: >25 IU/ml), RF, AKA and APF, MCV, and GPI. All the anti-CCP antibodies and/or anti-AKA/APF/MCV antibody-negative RA patients satisfy the diagnostic criteria of ultrasound or MRI about RA synovitis. The study was approved by ethics committees of Peking Union Medical College Hospital Review Board.

Example 1 Identification of Candidate RA Autoantigens Using High-Density Protein Chips

The high-density protein chips and Saccharomyces cerevisiae-expressing recombinant vectors including target gene sequences were provided by Dr. Zhu's laboratory at Johns Hopkins University. Each chip consisted of 48 blocks and the block included 992 probe points arranged in a 32*31 array, with 2 parallel points for each protein probe. The protein chip consisted of 21827 non-redundant recombinant human proteins. The recombinant proteins, with glutathione S-transferase (GST) tag at the N-terminus, were derived from the full-length open reading frame (ORF) of the corresponding gene expressed by Saccharomyces cerevisiae.

The quality of chips was verified by hybridizing mouse anti-GST monoclonal antibodies with the chips. Qualified repeatability of duplicate protein spots was achieved when the correlation coefficient of fluorescent signal value between duplicate spots reached 97%.

Each high-density protein chip included 47616 protein spots (including positive control and negative control; each protein antigen included two parallel points). The chip consisted of 21827 non-redundant recombinant human proteins. All proteins on each chip consisted of 48 blocks and each block was arranged in a 32*31 array. For all the recombinant protein probes carried GST tag at the N-terminus, mouse anti-GST monoclonal antibodies were used for detection of all probes at the chip, in order to make sure that the majority of recombinant proteins at the chip for serum identification at the chip were detectable and two parallel points on the same probe had high parallelism. As shown in FIG. 1, GST tag-positive points detected at the chip appear to be red (white when the signal is saturated). Each protein chip consisted of 48 blocks and all protein probes in each block was arranged in a 32*31 array, and each probe consisted of two parallel points (left point and right point). Each chip consisted of 21827 non-redundant recombinant proteins and other control probes. All recombinant proteins carried GST tag. FIGS. 1A and 1C show the scan image of the whole chip and single block respectively, using mouse anti-GST monoclonal antibodies for detection. FIG. 1B shows the distribution of all probes' signal to noise ratio (SNR). The probe point was considered to be detectable when the SNR of two parallel points was greater than 3. According to the standard, 96.8% of the proteins were detectable (FIG. 2).

Example 2 Hybridization of High-Density Protein Chips, RA and Control Serum

60 RA and 60 control (10 BD, 10 TA, 10 SLE and 30 healthy controls) serum samples were hybridized with 120 protein chips, and candidate RA autoantigens were identified by signal collection and data analysis. PE-Cy5 labeled anti-human IgG antibody was used to detect the reaction between the serum autoantibodies and autoantigen probes. FIG. 3 shows the representative partial scan image formed by serum hybridization with high-density protein chips, different protein antigen probe is shown in the box. A, C, E, G show scan images of hybridization of 4 RA serum samples with chips. B, D, F, H show scan images of hybridization of 4 control serum samples (including disease and healthy controls) with chips. FIG. 1 shows the scan image of RA treatment effective. Figure J shows the scan image of RA treatment ineffective. Two parallel points protein probes in the boxes of Figures A and B are DOHH, DUSP11 in the boxes of Figures C and D, PTX3 in the boxes of Figures E and F, PAGE5 in the boxes of Figures G and H, ERH in the boxes of Figures I and J. In general, serum from RA, disease control (BD, SLE, TA), or healthy group only recognizes a small part of proteins at the chip. And positive signal can also be detected in chips of normal control serum, suggesting autoantibodies can exist in healthy group, but these autoantibodies do not lead to diseases.

The fluorescence signal images of each chip obtained by scan and the template file of the chip, i.e. gail files were dragged to GenePix Pro 6.0 for one to one correspondence. All probe signal information of each chip collected by GenePix Pro 6.0 was transformed and saved in excel format The signal value was calculated by the ratio of foreground (F635 median) to background (B635 median) signals. i.e. I ij=F635median/B635median (I ij represented the signal value of protein point i in block j). As the protein antigen probe signal value was closer to 1, the corresponding autoantibody in serum became less detectable. Higher signal value meant the stronger ability of autoantibodies to bind the target protein antigen probe.

To eliminate the hybridization differences caused by different chips or different space in the same chip, within-chip normalization was adopted to normalize the intra-array signal intensity, which means we hypothesized that all target proteins were placed on the substrate at random, and only less 5% of target proteins as autoantigens were identified and detected by corresponding target antibody. Consequently, the signal distribution at the chips was random and remained consistent between different blocks. The median of all the probe point signal value was set as 1 to normalize the probe point signal value in different blocks. Ĩ ij=I ij−median(I j)+1 (median(I j) represented the median of all points signal value in the block j, I ij represented the signal value of protein point i in the block j after normalization.

On this basis, according to the method of paper (Hu S, Xie Z, Onishi A, Yu X, Jiang L, Lin J, Rho H S, Woodard C, Wang H, Jeong J S, Long S, He X, Wade H, Blackshaw S, Qian J, Zhu H, Profiling the human protein-DNA interactome revealed ERK2 as a transcriptional repressor of interferon signaling. Cell 2009; 139: 610-622), the cutoff was set to identify the positivity of all probe points, i.e. calculating the mean of all point signal value at whole chip (I average), setting the standard deviation (SD) of signal values less than 1; setting I average +5SD as cutoff to analyze the positivity of probe points at the chip; collecting the positivity information of immune reaction between each serum with each protein antigen probe, and using chi-square test (X2) or Fisher exact test to determine the candidate RA autoantigen.

For the identification of ACPA-negative RA candidate markers, antigens with specificity more than 90% and sensitivity more than 25% served as candidate RA autoantigens. For the identification of candidate biomarkers predicting disease activity and treatment efficacy, if P<0.05 (calculated by chi-square test or Fisher exact test), it will be included in candidate markers.

The candidate target autoantigens of interest at the chip were determined by data analysis. For whether the on-chip protein probe was a RA-specific autoantigen, or whether it is a disease-associated or therapeutically relevant autoantigen, the X2 test or Fisher's exact test was used to determine that the protein was a target protein antigen for the ACPA-negative specific reaction in RA. In the present invention, 35 antigens with a specificity of 90% and a sensitivity of more than 25% were used as candidate ACPA-negative RA autoantigens, and 7 proteins were candidate autoantigens for predicting disease activity, and 6 proteins were candidate autontigens for predicting therapeutic efficacy (wherein two protein candidate antigens were repeated in different sets of analyses), see Table 1 for details.

TABLE 1-1

Small sample sera were hybridized with high-density protein chips to identify 35 candidate ACPA-negative RA-specific autoantigens

Number of
Number of
Number of
Number of
Number of

positive
positive
positive
positive
positive

probes
probes
probes
probes
probes

identified
identified
identified
identified
identified

Abbreviation

in 30 CCP-
in 30 CCP-
in 60 RA
in 30 disease
in 30 healthy

of name of

RA serum
RA serum
serum
control
control

proteins
ID No.
Antigen
Name of proteins
group
group
group
group
group

DOHH
NM_031304.2
newly
Deoxyhypusine dioxygenase
9
10
19
1
2

identified

DUSP11
BC000346.2
newly
Dual specificity protein
11
12
23
0
0

identified
phosphatase 11

PTX3
NM_002852.3
newly
Pentaxin-related protein PTX3
12
13
25
0
1

identified

STK3
NM_006281.2
newly
Serine/threonine- protein
13
20
33
0
1

identified
kinase Krs-1

HDAC4
BC039904.1
newly
Histone deacetylase 4
12
19
31
0
1

identified

RAI14
BC052988.1
newly
Ankyrin repeat and coiled-coil
12
19
31
0
1

identified
structure-containing protein

FGF12
BC022524.1
newly
Fibroblast growth factor
11
16
27
0
2

identified
homologous factor 12

RAB35
NM_006861.4
newly
Ras-related protein Rab-35
12
15
27
0
1

identified

APH1A
NM_016022.2
newly
Gamma-secretase subunit
10
15
25
0
0

identified
APH-1A

CHAC2
NM_001008708.1
newly
Putative glutathione-specific
14
14
28
0
1

identified
gamma-glutamylcyclo-

transferase 2

ND
BC000566.2
newly

Homo sapiens RAB,
14
14
28
0
2

identified
member of RAS

oncogene family-like 4

TBC1D19
ENST00000264866
newly
TBC1 domain family
12
14
26
0
2

identified
member 19

NECAB1
NM_022351.2
newly
N-terminal EF-hand calcium-
9
14
23
2
1

identified
binding protein 1

AK2
NM_001625.2
newly
Adenylate kinase 2
12
13
25
0
0

identified

ERH
NM_004450.1
newly
Enhancer of rudimentary
11
13
24
0
2

identified
homolog

ATP13A5
NM_193505
newly
Probable cation-transporting
14
12
26
1
2

identified
ATPase 13A5

PAGES
NM_001013435.1
newly
P antigen family member 5
11
12
23
1
2

identified

SUGT1
NM_006704.2
newly
Suppressor of G2 allele of
11
12
23
1
2

identified
SKP1 homolog

TABLE 1-1

Small sample sera were hybridized with high-density protein chips to identify 35 candidate ACPA-negative RA-specific autoantigens

Number of
Number of
Number of
Number of
Number of

positive
positive
positive
positive
positive

probes
probes
probes
probes
probes

identified
identified
identified
identified
identified

Abbreviation

in 30 CCP-
in 30 CCP-
in 60 RA
in 30 disease
in 30 healthy

of name of

RA serum
RA serum
serum
control
control

proteins
ID No.
Antigen
Name of proteins
group
group
group
group
group

MYLK
NM_053031.2
newly
Myosin light chain kinase
10
12
22
2
2

identified

NDRG1
NM_006096.2
newly
N-myc downstream-regulated
9
12
21
0
0

identified
gene 1 protein

CHST11
NM_018413.2
newly
Carbohydrate sulfotransferase 11
9
12
21
0
1

identified

STK24
BC065378.1
newly
Serine/threonine- protein
9
12
21
1
1

identified
kinase 24

ND
NM_002720.1
newly

Homo sapiens protein
9
11
20
0
0

identified
phosphatase 4

catalytic subunit (PPP4C)

RAB3D
NM_004283.2
newly
Ras-related protein Rab-3D
9
11
20
0
0

identified

POLR3B
BC046238.1
newly

Homo sapiens polymerase
9
10
19
0
0

identified
(RNA) III polypeptide B,

mRNA

UBXN10
NM_152376.2
newly
UBX domain-containing
9
10
19
0
1

identified
protein 10

ATXN10
BC007508
newly
Spinocerebellar ataxia type 10
9
10
19
1
1

identified
protein

TNFAIP1
NM_021137.3
newly
Tumor necrosis factor, alpha-
10
9
19
2
0

identified
induced protein 1, endothelial

METTL21C
NM_001010977.1
newly
Protein-lysine methyltransferase
9
9
18
0
1

identified
METTL21C

NDEL1
BC026101.2
newly
Nuclear distribution protein
9
9
18
1
1

identified
nudE-like 1

LSP1
BC001785.1
newly
Lymphocyte-specific protein 1
9
9
18
2
1

identified

BABAM1
NM_001033549.1
newly
BRISC and BRCA1-A complex
11
7
18
0
1

identified
member 1

DGKK
NM_001013742.2
newly
Diacylglycerol kinase kappa
10
7
17
2
2

identified

PPFIA4
NM_015053.1
newly
Protein tyrosine phosphatase
9
7
16
2
0

identified
receptor type f polypeptide-

interacting protein alpha-4

PDCD2
NM_002598.2
newly
Programmed cell death protein 2
9
7
16
0
1

identified

TABLE 1-2

Small sample serum were hybridized with high-density protein chip to

identify 7 candidate autoantigens for predicting disease activity.

Number of positive probes
Number of positive probes

identified in 40 high
identified in 20 moderate to low

Name of proteins
activity RA serum group
activity RA serum group

Zinc finger and SCAN domain-containing protein 20
9
11

Protein FAM84A (Neurologic sensory protein 1) (NSE1)
7
9

Sorting nexin-33 (SH3 and PX domain-containing protein 3)
8
9

RNA polymerase I-specific transcription initiation factor RRN3
5
8

Pleckstrin homology domain-containing family G member 2
2
6

Nucleolar protein 3
3
6

RING finger protein 183
13
2

TABLE 1-3

Small sample serum were hybridized with high-density protein chip to identify

7 candidate autoantigens for predicting disease therapeutic efficacy

Number of positive probes
Number of positive probes

identified in 20 RA serum
identified in 20 RA serum

Name of proteins
group without therapeutic efficacy
group with therapeutic efficacy

Regulator of cell cycle RGCC
1
9

Tumor necrosis factor, alpha-induced protein 1, endothelial
7
4

Glycine-tRNA ligase
8
4

Sperm protein associated with the nucleus on the X chromosome N2
7
3

ADP-ribosylation factor like protein 2-binding protein
7
3

Enhancer of rudimentary homolog
8
14

Example 3 Construction of RA Autoantigen Protein Chip and Verification of Serum Screening

By analyzing the result of hybridizing small number of serum samples with high-density protein chips, 46 candidate RA autoantigens were identified. To verify the specificity and sensitivity of these autoantigens, the present invention constructed low probe density RA autoantigen protein chip. Table 2 shows the distribution of microarray of each probe at RA autoantigens protein chip. The probes at the chip included 46 candidate RA autoantigens and 5 control probes (IGHG1).

TABLE 2

Microarray of each probe at RA autoantigens protein chip

AK2
IGHG1
ND
ATP13A5
ND
TBC1D19

RAB35
UBXN10
RAB3D
APH1A
TNFAIP1
HDAC4

ARL2BP
RAI14
RRN3
POLR3B
ERH
NDRG1

BLANK
BLANK
BLANK
BLANK
BLANK
GARS

SUGT1
IGHG1
NOL3
ZSCAN20
LSP1
RGCC

EMPTY
PAGE5
FGF12
FAM84A
DOHH
NECAB1

NDEL1
DUSP11
PDCD2
MYLK
STK24
METTL21C

IGHG1
STK3
BABAM1
DGKK
PTX3
PPFIA4

EMPTY
SPANXN2
IGHG1
CHAC2
RNF183
ATXN10

IGHG1
EMPTY
CHST11
PLEKHG2
SNX33
BLANK

51 probes at RA autoantigen protein chip all had duplicate points. 14 microarrays were included at each substrate and every microarray was separated by the fence to form independent space before hybridization of serum and chip. Every chip can detect 14 serum samples at the same time. The large scale samples of serum hybridized with RA autoantigen chip included 290 RA, and 237 controls serum (9 OA, 38 SLE, 39 AS, 18 BD, 10 ANCA, 21 SS and 102 healthy controls serum). Genepix Pro6.0 was applied to acquire the information of probe points from the hybridization of RA autoantigen protein chip. The signal strength was calculated by the ratio of foreground to background signals of each probe point. The average of two parallel points hybridization signal of each probe was set as the signal value of hybridization of the probe and the serum for further analysis. Negative control protein pore signal was used to evaluate the quality of experiments. The prepared protein chip consisting of 46 candidate RA autoantigens included 6 blank control (BLANK) and 3 negative control (EMPTY). The average of negative control protein pore signal values was used for the quality assessment of the protein chip. The signal value of each block's negative control protein on each chip was collected for drawing a frequency distribution of signal values. As shown in FIG. 4, the signal value of the BLANK and EMPTY was around 1, indicating that the foreground value and background value of the point are nearly identical and signal values collected from the chips were rational and reliable.

Chi-square test (X2) or Fisher exact test were used to analyze data from ACPA-negative RA patients and healthy and disease controls, calculating T score, P value of every diagnostic marker protein. 1000 different cutoff values were selected for each protein, specificity and sensitivity can be calculated according to each cutoff value, these 1000 points (1-specificity, sensitivity) were used to draw the ROC curve, and the AUC was calculated. The cutoff that corresponded to the point with the maximum sum of sensitivity and specificity was the best cutoff. As shown in Table 3 and FIG. 5, in the hybridization results with large scale samples of serum, the sensitivity of immune reaction of four protein antigens with ACPA-negative RA serum was higher than 25%, and these four protein antigens had specificity different from healthy controls and disease controls (DOHH: 49.66%, PAGE5: 72.79%, DUSP11: 53.06%, PTX3: 43.54%). FIG. 5 shows the distribution of signal value of these two protein markers in RA patients and healthy controls and disease controls, indicating that autoantibodies expression in RA patients is higher than the controls.

TABLE 3

The cutoff and corresponding AUC of four proteins including DOHH in RA

Name
T Score
p value
FDR(BH)
Q Value
Fold Change
AUC
cutoff
Specificity
Sensitivity

PAGE5
−3.49914
6.00E−04
0.005056
0.001438
1.11134349
0.627525
1.830343
0.487437
0.727891

PTX3
−3.37216
6.00E−04
0.005056
0.001438
1.13017941
0.594742
2.104885
0.743719
0.435374

DOHH
−2.23377
0.020596
0.050632
0.01337
1.08083119
0.599221
2.02812
0.693467
0.496599

DUSP11
−1.79863
2.00E−04
0.002949
0.001038
1.24243701
0.612484
2.112003
0.668342
0.530612

Example 4 Analysis of the Newly-Identified Antigens for Predicting Disease Activity in RA Autoantigen Protein Chip

The T test was used to analyze data of two groups of patients with moderate to low activity and high activity, calculating T score, P value for each protein associated with predicting disease activity. Then 1000 different cutoff values were selected for each protein, specificity and sensitivity can be calculated according to each cutoff value, these 1000 points (1-specificity, sensitivity) were used to draw the ROC curve, and the AUC was calculated. The cutoff that corresponded to the point with the maximum sum of sensitivity and specificity was the best cutoff. As shown in Table 4 and FIG. 6, the AUC of RRN3 is highest, 0.65, when the cut off is 1.55. FIG. 6 shows the signal value distribution of groups with moderate to low activity and high activity, patients with high activity expressing more autoantigen than patients with moderate to low activity.

TABLE 4

The cutoff and corresponding AUC of RRN3 in RA patients with different disease activity

Fold
active
active
low
low

Name
Score
P
FDR(BH)
Q Value
Change
Mean
Std
Mean
Std
Cutoff
AUC
Sensitivity
Specificity

RRN3
5.49
2.00E−04
6.55E−04
0.000197
1.23
1.74
0.564
1.42
0.42
1.55
0.65
64.10%
69.40%

Further analysis of the clinical sub-group revealed that autoantigen PLEKHG2 could distinguish disease activity in ACPA-positive RA patients, but not ACPA-negative RA patients. When the cutoff was 1.548 for RRN3 and 1.172 for PLEKHG2, and the corresponding AUC was 0.845 and 0.817 respectively, indicating the great clinical value.

TABLE 5

The cutoff and AUC of RRN3 and PLEKHG2 in different disease activity group of ACPA-positive patients

CCP +
CCP +
ccp +
ccp +

Fold
low
low
active
active

Speci-
Sensi-

Name
Score
P
FDR(BH)
Q Value
Change
Mean
Std
Mean
Std
Cutoff
AUC
ficity
tivity

RRN3
−10.18
2.00E−04
5.62E−04
0.044524
1.522
1.237
0.254
1.883
0.504
1.548
0.845
91.70%
74.70%

PLEKHG2
−6.83
2.00E−04
5.62E−04
0.155012
1.444
1.132
0.21
1.634
0.652
1.172
0.817
79.20%
82.10%

Example 5 Analysis of the Newly-Identified Antigens for Predicting Disease Therapeutic Efficacy in RA Autoantigen Protein Chip

T test was used to analyze data from effective and non-effective RA patients, calculating T score, P value for each protein associated with predicting disease therapeutic efficacy. Then 1000 different cutoff values were selected for each protein, specificity and sensitivity can be calculated according to each cutoff value, these 1000 points (1-specificity, sensitivity) were used to draw the ROC curve, and the AUC was calculated. The cutoff that corresponded to the point with the maximum sum of sensitivity and specificity was the best cutoff. As shown in Table 6 and FIG. 8, when the cutoff was set at 1.201, the AUC was the largest, 0.733. FIG. 8 shows the signal value distribution of ERH in effective and non-effective patients, indicating that the autoantigen expressed in the effective patients are more than the non-effective patients.

TABLE 6

The cutoff and AUC of ERH in different efficacy group of RA patients

effec-
effec-
non-
non-

Fold
tive
tive
effective
effective

Sensi-
Speci-

Name
Description
Score
P
FDR(BH)
Q Value
Change
Mean
Std
Mean
Std
Cutoff
AUC
tivity
ficity

ERH
NM_004450.1
4.86
2.00E−04
0.003933
0.005899
1.341
1.733
0.545
1.292
0.446
1.201
0.733
80.8%
68.7%

The description above is only a preferred practice of the present invention, and it should be noted that the skilled person in the art can make improvements and modifications without departing from the technical principles of the present invention. These improvements and modifications should also be considered as the scope of protection of the present invention.

ACPA-NEGATIVE RA DIAGNOSTIC MARKER AND APPLICATION THEREOF

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