BioMed Research International

BioMed Research International / 2016 / Article

Research Article | Open Access

Volume 2016 |Article ID 3290260 | 29 pages | https://doi.org/10.1155/2016/3290260

iTRAQ-Based Proteomics Identification of Serum Biomarkers of Two Chronic Hepatitis B Subtypes Diagnosed by Traditional Chinese Medicine

Academic Editor: Yasunobu Matsuda
Received18 Jul 2016
Accepted24 Oct 2016
Published29 Nov 2016

Abstract

Background. Chronic infection with hepatitis B virus (HBV) is a leading cause of cirrhosis and hepatocellular carcinoma. By traditional Chinese medicine (TCM) pattern classification, damp heat stasis in the middle-jiao (DHSM) and liver Qi stagnation and spleen deficiency (LSSD) are two most common subtypes of CHB. Results. In this study, we employed iTRAQ proteomics technology to identify potential serum protein biomarkers in 30 LSSD-CHB and 30 DHSM-CHB patients. Of the total 842 detected proteins, 273 and 345 were differentially expressed in LSSD-CHB and DHSM-CHB patients compared to healthy controls, respectively. LSSD-CHB and DHSM-CHB shared 142 upregulated and 84 downregulated proteins, of which several proteins have been reported to be candidate biomarkers, including immunoglobulin (Ig) related proteins, complement components, apolipoproteins, heat shock proteins, insulin-like growth factor binding protein, and alpha-2-macroglobulin. In addition, we identified that proteins might be potential biomarkers to distinguish LSSD-CHB from DHSM-CHB, such as A0A0A0MS51_HUMAN (gelsolin), PON3_HUMAN, Q96K68_HUMAN, and TRPM8_HUMAN that were differentially expressed exclusively in LSSD-CHB patients and A0A087WT59_HUMAN (transthyretin), ITIH1_HUMAN, TSP1_HUMAN, CO5_HUMAN, and ALBU_HUMAN that were differentially expressed specifically in DHSM-CHB patients. Conclusion. This is the first time to report serum proteins in CHB subtype patients. Our findings provide potential biomarkers can be used for LSSD-CHB and DHSM-CHB.

1. Introduction

Chronic hepatitis B virus (CHB) infection is a leading cause of cirrhosis and hepatocellular carcinoma (HCC) and, in addition to morbidity and mortality, creates significant economic and social burdens [1, 2]. It is estimated that approximately 240 million people have CHB infection worldwide and CHB infection should be responsible for 650,000 cases of hepatocellular carcinoma [2, 3]. Due to the pathogenicity of CHB, early detection of CHB infection is the goal of treatment to diagnose and prevent the progression [4]. To this end, several hepatitis B virus (HBV) markers have been identified, including antigens (hepatitis B surface antigen, HBsAg; hepatitis Be antigen, HBeAg; hepatitis B core antigen, HBcAg), antibodies (hepatitis surface antibody, anti-HBs; hepatitis Be antibody, anti-HBe; hepatitis B core antibody, anti-HBc), and immunoglobulin (Ig) G and immunoglobulin M; however, unequivocal diagnosis requires more biomarkers [5].

By traditional Chinese medicine (TCM) pattern classification, CHB infected patients are accordingly classified into six subtypes [6]: (1) damp heat stasis in the middle-jiao (DHSM), (2) liver Qi stagnation and spleen deficiency (LSSD), (3) Yang deficiency of spleen and kidney (YDSK), (4) Yin deficiency of liver and kidney (YDLK), (5) blood stasis into collateral (BSIC), and (6) damp heat complicated with blood stasis (DHBS). Among them DHSM and LSSD are two most common CHB subtypes and have unique syndromes in clinic. For example, LSSD patients always have main syndromes, such as (Mi) flank pain and (Mii) abdominal distension and loose stools, and secondary symptoms, including (Si) depression and boredom, (Sii) body tired fatigue, and (Siii) pale tongue with teeth marks. DHSM patients have another two main syndromes, such as (M1) abdominal distension and (M2) yellow greasy moss, and three secondary syndromes, including (S1) nausea, being tired of the oil, and poor appetite, (S2) jaundice, bright color, and dark urine, and (S3) viscous stool foul smell. However, these syndromes are diagnosed by TCM doctors according to their experiences and the molecular biomarkers remain unclear.

Proteomics is a powerful technology recently developed to enhance our study on the diagnosis, treatment, and prevention of human diseases [7]. Among the proteomics technologies iTRAQ (isobaric Tags for Relative and Absolute Quantitation) has become popular for protein identification and quantification due to its sensitivity, accuracy, and high throughput [8]. It has been used to identify biomarker proteins for different stages of hepatitis B related diseases in patients and cellular models [912]. Several serum proteins have been reported to be potential biomarkers for CHB, such as actin [13], apolipoproteins A-I and A-IV [14], complement component [15], immunoglobulin related proteins [15, 16], haptoglobins β and α2 chain [14], and transferrin [17].

In this study, we employed iTRAQ combined with LC-ESI-MS/MS analyses to investigate protein biomarkers in the serum samples of two CHB subtype patients (LSSD and DHSM). Compared to healthy controls we found a number of proteins differentially expressed in both LSSD and DHSM CHB subtypes, such as actin, apolipoprotein, complement component, and immunoglobulin related proteins. In addition, we identified some proteins differentially expressed exclusively in one of LSSD and DHSM groups, such as gelsolin (GSN), likely SNC73 protein, and transient receptor potential cation channel subfamily M member 8 (TRPM8) that were found with different expression in LSSD-CHB patients only and transthyretin (TTR), tubulin, and keratin types I and II that were differentially expressed in DHSM-CHB patients only. Our findings not only validate previously reported CHB protein biomarkers but also report for the first time protein biomarkers for LSSD and DHSM CHB subtypes. The output of this study gives a valuable resource for future HBV associated studies and provides new insights of traditional Chinese medicine on molecular level.

2. Materials and Methods

2.1. Ethics Statement

This study was conducted in compliance with the Declaration of Helsinki, the ethics approval was granted by the research medical ethics committee of Chengdu University of Traditional Chinese Medicine, and signed informed consent was obtained from all participants.

2.2. Patients and Serum Collection

A total of 104 CHB patients were enrolled from West China Hospital, Sichuan University, and filtered with strict clinical evaluation described below. For iTRAQ proteomics analysis, we obtained blood samples from 30 LSSD-CHB patients, 30 DHSM-CHB patients, and 20 healthy controls (HCTL). For western blot analysis, 9 LSSD-CHB patients, 9 DHSM-CHB patients, and 6 HCTL participants were enrolled. Serum was collected from blood sample (4 mL) following the manufacture’s protocol. Briefly, blood sample was incubated at room temperature for 2 h in vacutainer blood handling tube (Becton Dickinson, New Jersey, USA) and centrifuged for 10 min at 3,000 rpm and 4°C. Serum sample, which is the result supernatant, was transferred into a clean polypropylene tube and stored at −80°C.

2.3. Clinical Evaluation

The viral markers HBsAg, HBeAg, anti-HBs, anti-HBc, and anti-HBe were determined routinely in serum samples using standard procedures (AxSYM®; Abbott Laboratories, Rungis, France), as well as other molecular diagnostic markers like ALT (alanine transaminase), AST (aspartate aminotransferase), STB (serum total bilirubin), CB (conjugated bilirubin), UCB (unconjugated bilirubin), and HBV-DNA. Participants, who have hepatitis B history or HBsAg positive history for more than six months, were diagnosed as chronic HBV infection if they were positive to HBsAg and/or HBV-DNA. We used both western and Chinese medicine criteria to divide CHB patients into two groups. First, participants were satisfied with the following requirements: (1) serum HBsAg positive for over 6 months; (2) HBV-DNA positive; (3) continuous or repeated elevated serum ALT in last 12 months; (4) being 18~60 years old; (5) no planed move during the test. Then, LSSD-CHB and DHSM-CHB patients were diagnosed using the clinical symptoms mentioned before. CHB patients were diagnosed as LSSD-CHB when they met the criteria: (1) Mi and Mii; (2) Mi, Sii, and Siii; (3) Mii and Si. DHSM-CHB patients were diagnosed as follows: (1) M1 and M2; (2) M1, S1, and S2; (3) M2 and two of the secondary symptoms. We also filtered the patients when they satisfied one of the following criteria: (1) being associated with other types of hepatitis viruses or human immunodeficiency virus (HIV); (2) cirrhosis, malignancy; (3) being diagnosed with fulminant hepatitis (including acute, subacute, and chronic severe hepatitis); (4) being associated with drug or toxic liver, autoimmune hepatitis, and genetic-metabolic liver disease; (5) heart, lung, kidney, endocrine, blood, and other serious diseases; (6) pregnant women and lactating women; (7) mental disorders, in line with Chinese Classification of Mental Disorders Diagnosis (CCMD-3) standard; (8) other individuals not suitable for the cohort study.

2.4. Protein Preparation

Serum sample (200 μL) from each patient was processed to reduce the complexity by using ProteoMiner™ Kits (Bio-Rad Laboratories, Hercules, CA, USA). Then, the sample was eluted using Lysis buffer at pH 8.5 (2M Thiourea, 7M Urea, 4% CHAPS, and 40 mM Tris-HCl), reduced using 10 mM DTT at 56°C for 1 h, and alkylated using 55 mM IAM in darkness for 1 h. After being precipitated within chilled acetone (4 × volume) at −20°C overnight, the protein sample was centrifuged at 30,000 ×g for 15 min at 4°C; the pellet was next dissolved in 500 μL of 0.5 M triethylammonium bicarbonate (Applied Biosystems, Milan, Italy) and sonicated at 200 W in ice for 15 min. Finally, the samples were centrifuged again at 30,000 ×g for 15 min at 4°C, and the supernatant was quantified using Bradford Protein Assay Kit (CWBIO, Beijing, China) and stored at −80°C for subsequent analysis.

2.5. iTRAQ Sample Labelling, SCX Fractionation, and LC-ESI-MS/MS Analysis

Proteins isolated from 10 individuals in the same group were pooled for iTRAQ labelling. Pooled protein samples (100 μg) were digested using Trypsin Gold (Promega, Madison, WI, USA) at 37°C for 16 h (protein: trypsin = 30 : 1). Digested peptides were dried by vacuum centrifugation, reconstituted in 0.5 M triethylammonium bicarbonate (Applied Biosystems, Milan, Italy), and processed 8-plex iTRAQ (Applied Biosystems) labelling following the protocols. Samples were labelled with the iTRAQ tags as follows: LSSD-CHB (113, 115, and 117), DHSM-CHB (114, 116, and 118), and HCTL (119 and 121). After being incubated at room temperature for 2 h, all the peptide mixtures were then pooled and dried by vacuum centrifugation. Strong cation exchange (SCX) chromatography was performed using the LC-20AB HPLC Pump system (Shimadzu, Kyoto, Japan), as previously described [18].

SFX fractions were resuspended in buffer A (2% ACN, 0.1% FA), followed by a centrifugation at 20,000 g for 10 min. Then, 10 μL of the supernatant was loaded onto a 2 cm C18 trap column on a LC-20AD nanoHPLC (Shimadzu, Kyoto, Japan) by the autosampler and eluted onto a 10 cm analytical C18 column (inner diameter 75 μm) packed in-house. At 300 nL/min the samples were loaded with buffer B (98% ACN, 0.1% FA) as the following procedural: 5% B for 1 min, a 44 min gradient from 2 to 35% B, a 2 min linear gradient to 80%, and 80% B for 4 min. Finally, the chromatographic conditions were restored in 1 min. Data acquisition was performed with an Q EXACTIVE (Thermo Fisher Scientific, San Jose, CA) coupled online to the HPLC, as described [19, 20].

2.6. Database Search and Protein Quantification

Database search and protein quantification were performed using Mascot (Matrix Science, London, UK; version 2.4.0). Briefly, raw data files acquired from the Orbitrap were converted into mascot generic format (MGF) files using msconvert tool of ProteoWizard (http://proteowizard.sourceforge.net/) [21]. To identify expressed proteins and quantify them, all 20 MGF files were merged and searched against UniProtHUMAN (2016_04, 152,544 sequences) database using Mascot with parameters: quantification: iTRAQ 8plex (Applied Biosystems iTRQA™ 8-plex); enzyme: trypsin; fixed modification: carboxymethyl (C), iTRAQ8plex (N-term) and iTRAQ8plex (K); variable modifications: dioxidation (M), oxidation (M), and iTRAQ8plex (Y), mass values: monoisotopic; peptide mass tolerance: ±15 ppm; fragment mass tolerance: ±20 mmu; max missed cleavages: (1) The charge states of peptides were set to +2 and +3. Specifically, an automatic decoy database search was performed in Mascot by choosing the decoy checkbox in which a random sequence of database is generated and tested for raw spectra as well as the real database. To reduce the probability of false peptide identification, only peptides at the 95% confidence interval by a Mascot probability analysis greater than “identity” were counted as identified. And each confident protein identification involves at least one unique peptide.

2.7. Protein Different Expression and Functional Analysis

To identify differentially expressed proteins in LSSD-CHB and DHSM-CHB compared to HCTL, we set a cut-off for fold change (>1.2) of protein abundance provided by Mascot and value (<0.05) calculated by edgeR [22]. Venn diagram of up- and downregulated proteins was analyzed by InteractiVenn (http://www.interactivenn.net/) [23]. To annotate potential functions of proteins, UniProt IDs of candidate proteins were submitted to DAVID Bioinformatics Resources 6.7 (https://david.ncifcrf.gov/home.jsp) [24] and STRING v10 (http://string-db.org/) [25], Gene Ontology (GO), and KEGG pathway were selected, and we used false discovery rate (FDR) to control the results. Protein-protein interaction networks were analyzed by STRING.

2.8. Western Blot Analysis

Protein samples obtained from serum of 9 LSSD-CHB patients, 9 DHSM-CHB patients, and 6 healthy individuals were resolved by 12% SDS-PAGE using Miniprotean II electrophoresis unit (Bio-Rad) run at constant 120 V for 1 h and transferred to a PVDF membrane (Amersham Biosciences) under a constant voltage of 15 V for 20 min. The membranes were blocked with 5% skim milk powder in Tris-buffered saline with 0.05% Tween-20 (TTBS) for 1 h and probed in TTBS with primary antibodies (1 : 500, Santa Cruz Biotechnology, CA, USA), anti-PSMA7 (sc-166761), anti-PF4V (sc-367359), anti-PSMA6 (sc-271187), anti-SERPING1 (sc-377062), anti-ACTB (sc-8432), anti-AHSG (sc-137102), anti-CTSC (sc-74590), anti-PLTP (sc-271596), and anti-ALB (sc-46293), followed by incubation with secondary antibody (1 : 1000) for 1 h in darkness. All antibody incubations were carried out using gentle orbital shaking at room temperature. Western blots were washed five times in TTBS (5 min × 2 and 10 min × 3) after each incubation step and visualized with enhanced chemiluminescence (ECL, GE Healthcare) following the manufacturers’ instructions. Band intensities on the Western blots were quantified using ImageJ (Wayne Rasband, National Institutes of Health). Albumin was used as reference to calculate the relative intensity of each protein. Then, mean ± SD values of each protein in HCTL and patients were calculated and compared using GraphPad Prism (http://www.graphpad.com/).

2.9. Statistical Analysis

Statistical analysis including the calculation of mean value, standard deviation (SD), and students’ -test was performed by using GraphPad Prism (v 6.02). The Holm-Sidak method was used to calculate the statistical significance of multiple clinical diagnostic values.

3. Results

3.1. Diagnosis of the Patients

To study serum protein biomarkers in LSSD and DHSM CHB patients, we obtained a total of 80 participants, including 30 LSSD-CHB, 30 DHSM-CHB patients, and 20 healthy volunteers. As shown in Table 1 and Table S1 in Supplementary Material available online at http://dx.doi.org/10.1155/2016/3290260, mean ages of LSSD-CHB, DHSM-CHB, and HCTL were 30, 36.8, and 35.5 years, respectively. Except missing information of three, all patients were positive to HBsAg and anti-HBc. There were two LSSD-CHB patients positive to anti-HBs, and 9 LSSD-CHB and 12 DHSM-CHB patients positive to anti-HBe. HBV-DNA levels in the blood samples of LSSD-CHB and DHSM-CHB patients were ranged from ~ IU/mL and ~ IU/mL, respectively. It is interesting that hepatitis B viral load (HBV-DNA copies) was significantly different () in LSSD-CHB and DHSM-CHB patients. Next, we examined ALT, AST, STB, CB, and UCB levels in the blood samples of CHB patients. Mean values of these diagnosis biomarkers in the blood samples of LSSD-CHB and DHSM-CHB patients were similar. In addition, the levels of ALT and AST remained at a high level, compared to healthy individuals [26, 27], which confirmed their CHB infection.


DiagnosisUnitLSSD-CHB ()DHSM-CHB ()HCTL () value

Sex
Male241510
Female61510

AgeYears17~5618~6024~56
Mean age30.836.8336.15
Standard deviation (SD)10.52611.88511.554

Hepatitis B surface antigen (HBsAg)
Positive2829
Negative00

Hepatitis surface antibody (anti-HBs)
Positive20
Negative2529

Hepatitis Be antigen (HBeAg)
Positive2119
Negative79

Hepatitis Be antibody (anti-HBe)
Positive912
Negative1916

Hepatitis B core antibody (anti-HBc)
Positive2829
Negative00

Alanine transaminase (ALT)IU/L13.8~62734~6731.0
Mean ALT level190.153187.393
SD161.231177.618

Aspartate aminotransferase (AST)IU/L26.5~34528~5560.9999
Mean AST96.74142.427
SD71.699153.539

Serum total bilirubin (STB)umol/L10.1~48.636.5~109.51.0
Mean STB19.20820.643
SD8.92618.127

Conjugated bilirubin (CB)umol/L2.4~16.42.3~99.21.0
Mean CB6.9239.408
SD3.54217.208

Unconjugated bilirubin (UCB)umol/L6~34.133.3~29.31.0
Mean UCB12.28411.182
SD5.9514.921

HBV-DNAIU/mL + 03~1.12 + 04~9.400.0096
Mean HBV-DNA
SD

3.2. Protein Identification and Quantification by iTRAQ

Next, we quantified the serum proteins in these LSSD-CHB and DHSM-CHB patients using iTRAQ. Initially, a total of 371,034 spectra were generated by liquid chromatography coupled to mass spectrometry (LC-MS/MS) analysis. Of them, 98,243 spectra (5,591 unique peptides) were aligned to 842 proteins from 666 families. The mass distribution of identified proteins (Figure 1(a)) suggested by Mascot revealed 170 (98.69%) were above 10 kDa, of which 170 (20.19%) and 141 (16.75%) were 10 to 20 kDa and above 100 kDa, respectively. We also counted the proteins aligned with significant peptides, shown in Figure 1(b), and 547 (64.96%) proteins were aligned by two and more peptides. In addition, the distribution of protein sequence coverage is shown in Figure 1(c). Protein sequence coverage with 40~100%, 30~40%, 20~30%, 10~20%, and under 10% variation accounted for 8.79%, 14.25%, 17.70%, 23.28%, and 35.99%, respectively. In Figure 1(d), we showed correlation between two samples and found LSSD-CHB samples were closer to DHSM-CHB samples than HCTL.

3.3. Identification of Differentially Expressed Proteins

Differentially expressed proteins were defined as those showed greater than 1.2-fold change in relative abundance and a value < 0.05. Compared to HCTL we identified a total of 392 proteins differentially expressed (Table S2), of which 273 were identified in LSSD-CHB group and 345 in DHSM-CHB group. As shown in the volcano plots, we identified 172 upregulated and 101 downregulated proteins in LSSD-CHB group (Figure 2(a)) and 199 upregulated and 146 downregulated proteins in DHSM-CHB group (Figure 2(b)), compared to HCTL group. Venn diagram (Figure 2(c)) revealed LSSD-CHB and DHSM-CHB shared 142 upregulated and 84 downregulated proteins; 30 and 57 proteins were exclusively upregulated in LSSD-CHB and DHSM-CHB, respectively; 17 and 62 proteins were exclusively downregulated in LSSD-CHB and DHSM-CHB, respectively; and no protein was identified with upregulation in one CHB subtype but with downregulation in another.

3.4. Potential Biomarkers for CHB

The identification of proteins differentially expressed in LSSD-CHB and DHSM-CHB groups relative to the HCTL group was of interest as these could provide leads for potentially useful diagnostic and prognostic biomarkers. First, we examined those 142 commonly upregulated and 84 commonly downregulated proteins. As shown in Table 2, the largest upregulated protein family was immunoglobulin related protein, showing 20 upregulated and 3 downregulated proteins identified. In clinical immunology, levels of immunoglobulins especially IgG can be used to characterize viral hepatitis in patients [28, 29]. Four IgG subclasses (IgG1 to IgG4) differ in their heavy chain constant regions and have different effects on virus-cell fusion inhibition, virus neutralization, and overall course of infection, as have been reported for various viruses including HIV [30] and HBV [31]. Highly expressed proteins encoding heavy chains for immunoglobulins including IGHG1, IGHG3, IGHG4, and IGH@ have been reported with upregulation in HBV [32, 33] and HCC patients [34]. Other upregulated protein families such as heat shock protein, histone, ras-related protein, and von Willebrand factor identified in current study have also been reported in patients infected by HBV or hepatitis C virus (HCV) [3538]. The largest downregulated protein family was complement, 15 complement proteins downregulated in LSSD-CHB with 0.82- to 0.37-fold change and in DHSM-CHB with 0.77- to 0.31-fold change. Other protein families like insulin-like growth factor binding protein and serum amyloid protein were also decreased in CHB patients in comparison to HCTL group. In addition, several known upregulated proteins from other families in patients infected by HBV or HCV (Table 2), such as apolipoproteins (APOA2, APOB, and APOB-variant) [39, 40], A2M (alpha-2-macroglobulin) [41], alpha-actinin-3 (ACTN3) [42, 43], vimentin (VIM) [38], and putative uncharacterized proteins (DKFZp686N02209 and DKFZp686I04196) [34, 44, 45], were identified in LSSD-CHB and DHSM-CHB groups. The different expression of proteins in the serum of CHB patients indicates they may have functions in response of HBV and CHB processing and can be used as biomarkers in clinical diagnosis.


FamilyUniProt_IDGene_nameDescriptionNumber of significant matchesNumber of significant sequencesemPAILSSD-CHB versus HCTLSSDHS-CHB versus HCTL

Immunoglobulin related proteinsA0A087WV47_HUMANIGHG1Ig gamma-1 chain C region1541145.371.841.47
A0A087WYC5_HUMANIGHG1Ig gamma-1 chain C region1501144.821.871.48
A0A087X1C7_HUMANIGHG1Ig gamma-1 chain C region1511134.791.841.47
A0A087WXL8_HUMANIGHG3Ig gamma-3 chain C region739112.071.841.47
A0A0G2JPD4_HUMANIGHG4Ig gamma-4 chain C region (fragment)3161.561.691.24
KV112_HUMANIg kappa chain V-I region Kue220.531.821.51
KV311_HUMANIg kappa chain V-III region IARC/BL41210.491.611.28
LV302_HUMANIg lambda chain V-III region LOI2534.011.731.35
LV301_HUMANIg lambda chain V-III region SH610.611.991.56
S6B2B6_HUMANIgG H chain38430.62.051.57
S6BAM6_HUMANIgG H chain38940.92.051.56
S6BGE0_HUMANIgG H chain39441.132.041.56
S6C4S4_HUMANIgG H chain38430.732.051.57
S6C4R7_HUMANIgG L chain25766.681.531.27
Q6GMX6_HUMANIGH@IGH@ protein1524146.041.831.46
A0A0F7TC28_HUMANIGHV4-4IGHV4-4 protein (fragment)321.271.491.24
Q5FWF9_HUMANIGL@IGL@ protein14366.031.601.32
Q6PIK1_HUMANIGL@IGL@ protein19754.451.591.29
Q9UL84_HUMANMyosin-reactive immunoglobulin heavy chain variable region (fragment)631.691.521.46
Q9UL79_HUMANMyosin-reactive immunoglobulin light chain variable region (fragment)210.570.650.50
A0A0C4DH33_HUMANIGHV1-24Protein IGHV1-24 (fragment)520.840.820.81
A0A0A0MT74_HUMANIGKV1-16Protein IGKV1-16 (fragment)510.91.581.26
A0A075B6I9_HUMANIGLV7-46Protein IGLV7-46 (fragment)3131.411.541.36

ComplementB7Z1F8_HUMANcDNA FLJ53025, highly similar to complement C4-B22301256.680.780.77
B4E3S6_HUMANcDNA FLJ58413, highly similar to complement component C763101.740.550.50
A8K2T4_HUMANcDNA FLJ78207, highly similar to human complement protein component C7 mRNA86151.310.550.50
B2RA39_HUMANcDNA, FLJ94686, highly similar to Homo sapiens complement factor H-related 5 (CFHL5), mRNA3550.510.540.57
CO4A_HUMANC4AComplement C4-A58896521.280.790.75
CO4B_HUMANC4BComplement C4-B59836623.030.790.74
A0A024R035_HUMANC9Complement component 9, isoform CRA_a225175.120.670.54
CO6_HUMANC6Complement component C692120.830.500.48
CO8A_HUMANC8AComplement component C8 alpha chain6681.510.660.53
F5GY80_HUMANC8BComplement component C8 beta chain133163.280.650.61
CO8G_HUMANC8GComplement component C8 gamma chain4186.860.610.50
B1AKG0_HUMANCFHR1Complement factor H-related protein 121664.260.660.75
FHR3_HUMANCFHR3Complement factor H-related protein 34561.190.820.77
FHR4_HUMANCFHR4Complement factor H-related protein 43130.410.370.31
A0A0S2Z4I5_HUMANCFPComplement factor properdin isoform 1 (fragment)1320.170.580.72

ApolipoproteinAPOA2_HUMANAPOA2Apolipoprotein A-II42121.841.481.26
A0A0B4RUS7_HUMANAPOA5Apolipoprotein A-V, isoform CRA_a15710.730.62
E1B4S9_HUMANAPOBApolipoprotein B (fragment)129710.941.971.53
C0JYY2_HUMANAPOBApolipoprotein B (including Ag(X) antigen)522721521.891.841.44
Q59HB3_HUMANApolipoprotein B variant (fragment)16616916.331.851.41
B0YIW2_HUMANAPOC3Apolipoprotein C-III57758.480.660.55
APOC4_HUMANAPOC4Apolipoprotein C-IV2653.840.800.60

HistoneH15_HUMANHIST1H1BHistone H1.5420.352.021.72
A0A024R017_HUMANHIST1H2ACHistone H2A2142.274.673.63
C9J0D1_HUMANH2AFVHistone H2A1331.114.843.73
A0A024QZZ7_HUMANHIST1H2BDHistone H2B1241.154.583.38
B2R4P9_HUMANH3F3AHistone H3930.884.983.72
Q5TEC6_HUMANHIST2H3PS2Histone H3430.62.591.87
B2R4R0_HUMANHIST1H4JHistone H439513.274.473.41

Heat shock proteinA0A024RD80_HUMANHSP90AB1Heat shock protein 90 kDa alpha (cytosolic), class B member 1, isoform CRA_a1260.311.461.51
HS90A_HUMANHSP90AA1Heat shock protein HSP 90-alpha28100.551.581.65

Insulin-like growth factor binding proteinC1K3N3_HUMANIGFBP1Insulin-like growth factor binding protein 1 (fragment)320.220.610.60
A0A024R1U8_HUMANIGFBP4Insulin-like growth factor binding protein 4, isoform CRA_a210.10.660.66
A0A024R433_HUMANIGFBP5Insulin-like growth factor binding protein 5, isoform CRA_a320.180.830.80

Ras-related proteinA0A024R7I3_HUMANRAB8ARAB8A, member RAS oncogene family, isoform CRA_a1141.081.751.73
A0A024RB87_HUMANRAP1BRAP1B, member of RAS oncogene family, isoform CRA_a1041.661.851.96
RAB10_HUMANRAB10Ras-related protein Rab-10930.711.741.72
RB11B_HUMANRAB11BRas-related protein Rab-11B540.731.911.57
RAB1B_HUMANRAB1BRas-related protein Rab-1B1261.51.731.73
RB27B_HUMANRAB27BRas-related protein Rab-27B540.71.701.59
RAB7A_HUMANRAB7ARas-related protein Rab-7a1661.941.601.66

Serum amyloidD3DQX7_HUMANSAA1Serum amyloid A protein5959.880.530.40
SAA1_HUMANSAA1Serum amyloid A-1 protein4044.990.480.38
SAA2_HUMANSAA2Serum amyloid A-2 protein2444.990.480.36
SAMP_HUMANAPCSSerum amyloid P-component228815.230.830.70

von Willebrand factorL8E853_HUMANVWFvon Willebrand factor189380.981.681.41
VWF_HUMANVWFvon Willebrand factor186380.931.671.41

change provided by MASCOT.
values calculated by edgeR to show the significance of different expression.

We next analyzed the potential functions of commonly differentially expressed serum proteins in LSSD-CHB and DHSM-CHB groups using DAVID Bioinformatics Resources 6.7 [24] and STRING v10 [25]. Cellular component annotation (Figure 3(a)) showed 63 and 7 proteins were “extracellular region” (GO: 0005576, GO: 0005615, and GO: 0044421) and “lipids” (GO: 0032994 and GO: 0034358), respectively. However biological process annotation (Figure 3(b)) showed most of the differentially expressed proteins associated with immune response, including “acute inflammatory response” (GO: 0002526), “response to wounding” (GO: 0009611), “inflammatory response” (GO: 0006954), “complement activation” (GO: 0006956), “defense response” (GO: 0006952), “humoral immune response mediated by circulating immunoglobulin” (GO: 0002455), “immune effector process” (GO: 0002252), “B cell mediated immunity” (GO: 0019724), and “activation of immune response” (GO: 0002253). It has been well studied that immunological events are necessary to control hepatitis B virus (HBV) infection [46, 47]. In addition, KEGG pathway analysis also showed differentially expression proteins function mainly in the pathways of “complement and coagulation cascades” (hsa04610), “systemic lupus erythematosus” (hsa05322), “focal adhesion” (hsa04510), and “viral carcinogenesis” (hsa05203). Overall, differentially expressed proteins in both LSSD-CHB and DHSM-CHB groups have potential ability to be used as biomarkers.

3.5. Dysregulated Proteins Detected Exclusively in LSSD-CHB and DHSM-CHB

Next, we examined differentially expressed proteins exclusively in LSSD-CHB and DHSM-CHB groups. A total of 30 upregulated and 17 downregulated proteins were specifically identified in LSSD-CHB patient serum samples (Table 3). Among them 11 upregulated immunoglobulin related proteins, gelsolin (GSN), serum paraoxonase/lactonase 3 (PON3), likely SNC73 protein, transient receptor potential cation channel subfamily M member 8 (TRPM8), and several uncharacterized proteins (DKFZp686M08189, DKFZp686C02220, and DKFZp686K04218) attracted our attention due to their high abundance. Serum PON3 concentrations have been reported to increase in patients with CHB or cirrhosis and showed significant direct correlations with the degree of periportal abnormalities including fibrosis and with serum FAS (a marker of antiapoptosis) concentrations [48]; however, serum gelsolin level has been reported to reduce significantly in patients with acute liver failure (47%), myocardial infarction (69%), sepsis (51%), and myonecrosis (66%) [49]. Among the specifically downregulated serum proteins in LSSD-CHB patients fibulin-1 (FBLN1) is a tumor suppressor in hepatocellular carcinoma [50]. Proteins specifically differentially expressed in LSSD-CHB patients were predicted to function mainly in biological processes of “protein activation cascade” (GO: 0072376), “regulation of response to wounding” (GO: 1903034), “blood coagulation, fibrin clot formation” (GO: 0072378), “negative regulation of response to stimulus” (GO: 0048585), and “acute-phase response” (GO: 0006953).


UniProt_IDGene_nameDescriptionNumber of significant matchesNumber of significant sequencesemPAI

Upregulated
A0A024R6I9_HUMANSERPINA4Serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4, isoform CRA_a79123.791.78
A0A075B6K3_HUMANIGLV2-11Protein IGLV2-11 (fragment)810.91.43
A0A075B6K6_HUMANIGLV4-3Protein IGLV4-3410.511.54
A0A075B6N7_HUMANIGHA2Ig alpha-2 chain C region (fragment)8061.941.44
A0A0A0MS51_HUMANGSNGelsolin146162.421.51
A0A0B4J1V4_HUMANIGHV1-46Protein IGHV1-46 (fragment)210.231.44
A0N7J6_HUMANREV25-2 (fragment)220.471.92
A0N8J1_HUMANV(k)3 sequence of NG9 gene from fetal liver DNA (fragment)611.11.49
CPN2_HUMANCPN2Carboxypeptidase N subunit 294112.091.48
D3DNU8_HUMANKNG1Kininogen 1, isoform CRA_a91143.31.50
FETUA_HUMANAHSGAlpha-2-HS-glycoprotein5730.641.70
FETUB_HUMANFETUBFetuin-B930.291.65
HV208_HUMANIg heavy chain V-II region SESS210.212.27
ITB1_HUMANITGB1Integrin beta-1320.061.46
KV119_HUMANIg kappa chain V-I region Wes2122.161.52
KV308_HUMANIg kappa chain V-III region CLL410.491.65
LV204_HUMANIg lambda chain V-II region TRO720.961.59
PCYOX_HUMANPCYOX1Prenylcysteine oxidase 14891.891.43
PEDF_HUMANSERPINF1Pigment epithelium-derived factor2391.541.48
PON3_HUMANPON3Serum paraoxonase/lactonase 3179123.891.51
Q6MZX9_HUMANDKFZp686M08189Putative uncharacterized protein DKFZp686M0818912471.411.43
Q6N091_HUMANDKFZp686C02220Putative uncharacterized protein DKFZp686C02220 (fragment)7161.21.46
Q6ZVX0_HUMANcDNA FLJ41981 fis, clone SMINT2011888, highly similar to protein Tro alpha1 H,myeloma12571.381.43
Q7Z379_HUMANDKFZp686K04218Putative uncharacterized protein DKFZp686K04218 (fragment)12471.441.43
Q8TE63_HUMANImmunoglobulin light chain variable region (fragment)420.971.45
Q96K68_HUMANcDNA FLJ14473 fis, clone MAMMA1001080, highly similar to Homo sapiens SNC73 protein (SNC73) mRNA20591.771.45
Q9NPP6_HUMANImmunoglobulin heavy chain variant (fragment)12571.751.43
Q9UL83_HUMANMyosin-reactive immunoglobulin light chain variable region (fragment)1422.981.54
Q9UL89_HUMANMyosin-reactive immunoglobulin heavy chain variable region (fragment)1858.631.49
TRPM8_HUMANTRPM8Transient receptor potential cation channel subfamily M member 8320.041.60

Downregulated
A0A024QZK7_HUMANHK1Hexokinase50.030.82
A0A024R2X3_HUMANHYAL1Hyaluronidase120.550.73
A0A024R451_HUMANSERPINE2Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2, isoform CRA_a1781.050.83
A0A024RAG6_HUMANC1QAComplement component 1, q subcomponent, A chain, isoform CRA_a1241.080.75
A0A0S2Z3Y1_HUMANLGALS3BPLectin galactoside-binding soluble 3 binding protein isoform 1 (fragment)247144.170.71
A0A0S2Z4D4_HUMANPLP1Proteolipid protein 1 isoform 1 (fragment)210.110.40
ADT4_HUMANSLC25A31ADP/ATP translocase 4510.160.65
B1AHL2_HUMANFBLN1Fibulin-17480.920.78
CALU_HUMANCALUCalumenin1270.860.76
CFAH_HUMANCFHComplement factor H689314.020.83
LBP_HUMANLBPLipopolysaccharide-binding protein148113.180.79
LRP1_HUMANLRP1Prolow-density lipoprotein receptor-related protein 137200.160.83
LTBP1_HUMANLTBP1Latent-transforming growth factor beta-binding protein 11980.160.77
NUCB1_HUMANNUCB1Nucleobindin-11770.660.78
Q8NBH6_HUMANFibulin-1125112.250.75
Q9HCC1_HUMANSingle chain Fv (fragment)1020.960.79
THRB_HUMANF2Prothrombin1145186.650.78

change provided by MASCOT.
values calculated by edgeR to show the significance of different expression.

We also identified 57 upregulated and 62 downregulated proteins exclusively in DHSM-CHB patients (Table 4). Two IGL@ proteins (Q6GMX4_HUMAN and Q6PIQ7_HUMAN) were specifically upregulated in DHSM-CHB patients with 1.27-fold change. Transthyretin (TTR), upregulated 1.34-fold in DHSM-CHB, can be induced by hepatitis C virus and activate TGF-β signaling pathway with furin [51]. Interestingly, we found three members of tubulin (TUBA4A, TUBB1, and TUBB8) were upregulated only in DHSM-CHB patients compared with HCTL. Although there are few reports about tubulin and HBV, it is well known that 42 kDa tubulin alpha-6 chain fragment in well-differentiated hepatocellular carcinoma tissues is from patients infected with HCV [52]. In addition, we found actinin, alpha 1 (ACTN1), which can directly interact with HCV [53], GAPDH, which can bind to the HBV posttranscriptional regulatory element [54], and polymeric immunoglobulin receptor (PIGR), the main transporter of IgA [55], were upregulated in DHSM-CHB but not in LSSD-CHB. Among DHSM-CHB specifically downregulated proteins we identified three members of keratin type I (KRT9, KRT10, and KRT14) and another three members of keratin type II (KRT1, KRT2, and KRT6B). Although there is no evidence showing relation between these six keratin proteins with CHB or other liver diseases, variant keratins are associated with progression of fibrosis during chronic hepatitis C infection [56]. Differentially expressed proteins exclusively detected in DHSM-CHB patients were predicted to be involved in the biological processes of “immune system process” (GO: 0002376), “response to stress” (GO: 0006950), “defense response” (GO: 0006952), “immune response” (GO: 0006955), and “single-organism metabolic process” (GO: 0044710).


UniProt_IDGene_nameDescriptionNumber of significant matchesNumber of significant sequencesemPAI

Upregulated
A0A024R145_HUMANALDOBFructose-bisphosphate aldolase530.221.29
A0A024R1N1_HUMANMYH9Myosin, heavy polypeptide 9, nonmuscle, isoform CRA_a1790.131.43
A0A024R5H8_HUMANRAB6ARAB6A, member RAS oncogene family, isoform CRA_b830.571.43
A0A024R694_HUMANACTN1Actinin, alpha 1, isoform CRA_a20100.421.33
A0A024R6G3_HUMANFBLN5Fibulin 5, isoform CRA_b630.271.33
A0A024R9T1_HUMANhCG_39634HCG39634, isoform CRA_a220.261.49
A0A024RDB8_HUMANHPSEHeparanase, isoform CRA_a2360.551.36
A0A024RDL8_HUMANASLArgininosuccinate lyase isoform 11050.391.65
A0A087WT59_HUMANTTRTransthyretin17575.661.34
A0A087WUL0_HUMANTKFCTriokinase/FMN cyclase330.151.28
A0A0A0MSD0_HUMANSVEP1Sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1430.021.36
A0A0A0MT32_HUMANLIPALysosomal acid lipase/cholesteryl ester hydrolase210.091.38
A0A0C4DFP6_HUMANCRTAC1Cartilage acidic protein 1650.241.23
A0A0S2Z3F6_HUMANCETPCholesteryl ester transfer protein plasma isoform 1 (fragment)95143.561.36
A0A125QYY9_HUMANIBM-B2 heavy chain variable region (fragment)1220.831.42
A0N7I9_HUMANF5-20F5-20 (fragment)410.471.68
A2NYU9_HUMANHeavy chain Fab (fragment)210.481.29
A8K486_HUMANPeptidyl-prolyl cis-trans isomerase220.321.40
ADIPO_HUMANADIPOQAdiponectin2752.131.32
APOF_HUMANAPOFApolipoprotein F730.51.29
ASSY_HUMANASS1Argininosuccinate synthase430.181.49
ATPB_HUMANATP5BATP synthase subunit beta, mitochondrial1120.221.34
B3KTV0_HUMANcDNA FLJ38781 fis, clone LIVER2000216, highly similar to HEAT SHOCK COGNATE 71 kDa PROTEIN550.211.29
B4DQK4_HUMANcDNA FLJ53743, highly similar to tubulin alpha-3 chain2160.811.61
B4DVA7_HUMANBeta-hexosaminidase320.151.26
B7Z478_HUMANPSMB2Proteasome (prosome, macropain) subunit, beta type, 2, isoform CRA_b210.31.65
BPIB1_HUMANBPIFB1BPI fold-containing family B member 11160.511.28
BTD_HUMANBTDBiotinidase4761.121.54
CAMP_HUMANCAMPCathelicidin antimicrobial peptide210.291.43
CAND1_HUMANCAND1Cullin-associated NEDD8-dissociated protein 1210.021.36
CATD_HUMANCTSDCathepsin D210.131.28
DHSO_HUMANSORDSorbitol dehydrogenase430.321.67
FIBA_HUMANFGAFibrinogen alpha chain102222.361.36
G3P_HUMANGAPDHGlyceraldehyde-3-phosphate dehydrogenase1971.371.37
G3V5Z7_HUMANPSMA6Proteasome subunit alpha type740.581.44
HV310_HUMANIg heavy chain V-III region HIL310.51.48
HV320_HUMANIg heavy chain V-III region GAL3631.911.32
KV404_HUMANIg kappa chain V-IV region B173421.451.45
LDHB_HUMANLDHBL-lactate dehydrogenase B chain420.331.65