Proteomics for discovery of novel biomarkers for sarcoidosis.
To discover a novel biomarker for sarcoidosis, we performed quantitative high-throughput proteomics using LC-MS/MS, followed by SRM verification (Fig. 1A). EVs were isolated by SEC from serum samples of control subjects and patients with sarcoidosis (Table S1).16 The isolation of EVs was confirmed according to the MISEV2018 guidelines.17 EVs from both groups expressed the EV marker protein CD9 and were similar in shape and size, less than 100 nm (Fig. 1B). EVs were positive for flotillin-1, CD63, and CD9 and negative for calnexin and haptoglobin (Fig. 1C). In the nanoparticle tracking analysis, serum EVs from both groups were indistinguishable in size and number (Fig. 1D, E and F).
The non-targeted proteomics analysis of EVs identified 2,292 proteins. Of those, 42 proteins were significantly upregulated in patients with sarcoidosis, and 324 were downregulated (Fig. 2A, Table 1, and Table S3). A principal component analysis of EV protein abundance partially separated control subjects from patients with sarcoidosis (Fig. 2B). Identified proteins were present in the cytoplasm (51%), plasma membrane (29%), and extracellular space (6%; Fig. 2C). Notably, the Ingenuity Pathway Analysis (IPA) of the protein signature of sarcoidosis EVs revealed factors involved in antigen presentation, immune response, and inflammatory response (Fig. 2D). Both tumor necrosis factor-α and transforming growth factor β1 pathways ranked highly as upstream signaling factors, suggesting that the protein fingerprints of serum EVs from patients with sarcoidosis reflect not only disease characteristics, but also its pathogenesis (Fig. 2E). We visualized the network of functions and pathways of the 42 upregulated proteins using the Clue GO/Clue Pedia plugin from Cytoscape. The nominal significant (P < 0.05) pathways and associated proteins are shown in Fig. 2F. Protein-protein interaction analyses revealed that the 42 upregulated proteins were clustered in six functional groups including transfer of LPS from the LBP carrier to CD14 (37.5%) and antigen processing cross-presentation (12.5%).
Table 1
Significantly Upregulated Proteins in Extracellular Vesicles From Patients With Sarcoidosis Compared to Those From Healthy Subjects
Uniprot ID
|
Description
|
Fold change
|
P-value
|
P36222
|
Chitinase-3-like protein 1
|
∞
|
0.032
|
O60704
|
Protein-tyrosine sulfotransferase 2
|
∞
|
0.033
|
Q9NZM1
|
Myoferlin
|
∞
|
0.004
|
Q7RTS3
|
Pancreas transcription factor 1 subunit alpha
|
∞
|
0.024
|
Q9Y230
|
RuvB-like 2
|
∞
|
0.034
|
Q8TAY7
|
Protein FAM11 D
|
∞
|
0.047
|
Q92522
|
Histone H1x
|
∞
|
0.038
|
P01040
|
Cystatin-A
|
∞
|
0.040
|
P06732
|
Creatine kinase M-type
|
∞
|
0.049
|
P98171
|
Rho GTPase-activating protein 4
|
∞
|
0.014
|
P36269
|
Glutathione hydrolase 5 proenzyme
|
∞
|
0.007
|
A8MVU1
|
Putative neutrophil cytosol factor 1C
|
∞
|
0.040
|
P14598
|
Neutrophil cytosol factor 1
|
∞
|
0.040
|
A6NI72
|
Putative neutrophil cytosol factor 1B
|
∞
|
0.040
|
Q8NCG7
|
Sn1-specific diacylglycerol lipase beta
|
∞
|
0.004
|
Q8N5C1
|
Protein FAM26E
|
∞
|
0.048
|
O15357
|
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
|
∞
|
0.019
|
Q75V66
|
Anoctamin-5
|
∞
|
0.045
|
Q14406
|
Chorionic somatomammotropin hormone-like 1
|
12.92
|
0.015
|
A5YKK6
|
CCR4-NOT transcription complex subunit 1
|
11.77
|
0.027
|
Q9BYX4
|
Interferon-induced helicase C domain-containing protein 1
|
7.52
|
0.008
|
Q6A163
|
Keratin, type I cytoskeletal 39
|
5.78
|
0.019
|
P20963
|
T-cell surface glycoprotein CD3 zeta chain
|
5.53
|
0.030
|
Q15256
|
Receptor-type tyrosine-protein phosphatase R
|
5.22
|
0.007
|
O14815
|
Calpain-9
|
4.22
|
0.032
|
P42574
|
Caspase-3
|
4.15
|
0.001
|
Q10588
|
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2
|
3.83
|
0.018
|
A0A075B6K4
|
Immunoglobulin lambda variable 3 − 1
|
3.74
|
0.013
|
Q92928
|
Putative Ras-related protein Rab-1C
|
3.38
|
0.048
|
Q3MII6
|
TBC1 domain family member 25
|
3.24
|
0.025
|
P24941
|
Cyclin-dependent kinase 2
|
2.72
|
0.039
|
Q8IU81
|
Interferon regulatory factor 2-binding protein 1
|
2.55
|
0.038
|
Q96JQ0
|
Protocadherin-16
|
2.26
|
0.044
|
Q9Y5X9
|
Endothelial lipase
|
2.26
|
0.024
|
P58166
|
Inhibin beta E chain
|
2.26
|
0.042
|
P15291
|
Beta-1,4-galactosyltransferase 1
|
1.91
|
0.024
|
P26572
|
Alpha-1,3-mannosyl-glycoprotein
2-beta-N-acetylglucosaminyltransferase
|
1.89
|
0.012
|
P18428
|
Lipopolysaccharide-binding protein
|
1.79
|
0.004
|
P02766
|
Transthyretin
|
1.78
|
0.027
|
P08571
|
Monocyte differentiation antigen CD14
|
1.71
|
0.019
|
P04003
|
C4b-binding protein alpha chain
|
1.67
|
0.041
|
Q9UK55
|
Protein Z-dependent protease inhibitor
|
1.58
|
0.019
|
Subsequently, we selected 25 proteins, taking into consideration of previous reports, in the validation cohort using SRM (Fig. 3A, Table S2, and Table S4). Targeted proteomics enables the efficient and specific verification of biomarker candidates without requiring antibodies and is, thus, a powerful tool for biomarker validation.14,15,20 Among 25 biomarker candidates, the expression levels of LBP and the monocyte differentiation antigen CD14 were markedly elevated in patients with sarcoidosis (Fig. 3B). Consistent with these findings, LPS signaling is highly ranked in the IPA upstream analysis (Fig. 1F), suggesting that these proteins are involved in sarcoidosis pathogenesis. Although serum levels of CD14 were elevated in patients with sarcoidosis,22 we did not observe this difference in free serum levels of both CD14 and LBP, in contrast to the EV levels, measured by ELISA (Fig. 3C). Analyses in KeyMolnet revealed that both CD14 and LBP were closely linked upstream and downstream to key molecules related to granuloma formation (Fig. 3D).
The presence and upregulation of these proteins were subsequently confirmed by western blotting (Fig. 4A) and immunoelectron microscopy (Fig. 4B), respectively. Furthermore, we confirmed the presence of CD14 and LBP in serum EVs isolated by both ultracentrifugation and the phosphatidylserine affinity method (data not shown).
The expression of CD14 and LBP in vivo and in vitro.
We also assessed the expression levels of these proteins in vivo by immunostaining of tissue samples. CD14 and LBP were weakly expressed in mononuclear cells in the lung and lymph nodes of healthy control subjects. By contrast, the expression of CD14 and LBP was strikingly increased in granulomatous lesions, especially in multinucleated giant cells (MGCs) and surrounding mononuclear cells (Fig. 5A and B). MGCs, the hallmarks of granuloma, are generated by monocytes in response to various stimuli, including LPS.23 To observe the dynamic changes of CD14 and LBP during MGC formation in vitro, we stimulated RAW 264.7 cells with LPS. Consistent with the in vivo results showing that CD14 was upregulated in macrophages, CD14 levels in EVs from cell culture supernatants were significantly elevated (Fig. 5C). Moreover, the LBP levels in EVs were also elevated, although these levels were unaltered in LPS-stimulated macrophages. Taken together, both CD14 and LBP were upregulated in the process of granuloma formation in vitro and in vivo. Moreover, given that in macrophages, the tetraspanin CD9 is closely colocalized with CD14, thereby inhibiting LPS-induced signaling,24 and that CD9 is strongly involved in macrophage fusion into MGCs,25 CD14 in macrophages and EVs might actively participate in the pathogenesis of granulomatous diseases (Fig. 5D).
Diagnostic potential of CD14 and LBP in serum EVs for sarcoidosis.
To further evaluate the diagnostic potential of the identified biomarkers, we analyzed their AUC values. The AUC values for CD14 and LBP were 0.81 and 0.84, respectively (Fig. 6A). Considering that most of the previously reported biomarkers appear to have some limitations in terms of sensitivity and specificity, it is intriguing to investigate different combinations. By combining the novel biomarkers with ACE, sIL-2R, and both, the AUC values could be increased further to 0.96, 0.96, and 0.98, respectively (Fig. 6B and Figure S1). Although LBP was weakly correlated with clinical parameters such as ACE (r: 0.45; P < 0.01), Krebs von den Lungen-6 (r: 0.35; P < 0.05), and C-reactive protein (r: 0.60; P < 0.01), the level of CD14 was not correlated with any parameters including monocyte number (Table S5). Although 59.6% of patients were ACE-negative, as many as 45.1% and 48.3% of ACE-negative patients could be further diagnosed by CD14 and LBP, respectively. Similarly, 46.8% of patients were sIL-2R-negative, and 40.8% and 45.5% of sIL-2R-negative patients could be further diagnosed by CD14 and LBP, respectively (Fig. 6C). These findings suggest that our novel biomarkers possess distinct properties in comparison to conventional biomarkers.
To further assess the potential of the novel biomarkers to monitor treatment response, we compared their levels in three patients with sarcoidosis before and after steroid administration. The CD14 and LBP levels in serum EVs of these patients decreased remarkably after therapy (Figure S2), suggesting that they could also serve as therapeutic biomarkers.