Clinical presentation and cytokine detection
The demographic and clinical characteristics of 41 NMOSD patients, 12 MS patients, and 34 HC are described in Table 1. Magnetic resonance imaging (MRI) and optical features of NMOSD are described in Supplementary Table 1.
Table 1. Clinical presentation of NMOSD patients, MS patients, and HC
|
HC
|
NMOSD
|
MS
|
Age (Mean ± SEM)
|
41.88 ± 2.385
|
41.20 ± 2.429
|
32.83 ± 4.071
|
Number
|
34
|
41
|
12
|
Sex, female:male
|
17:17
|
36:5
|
4:8
|
EDSS
|
n/a
|
2.83
|
1.83
|
AQP-4+ %
|
n/a
|
78.0 %
|
0 %
|
EDSS: expanded disability status scale
The relative levels of 200 unique proteins were measured using antibody arrays, and the resulting data were subjected to two parallel analyses: differential expression analysis and co-expression network analysis (Figure1a). The co-expression network analysis aimed to integrate both molecular and clinical data.
The statistical significance and fold change of the protein levels between NMOSD patients and HCs are displayed in a volcano plot (Figure1b). Expression levels of 39 cytokines of 200 proteins measured differed between NMOSD patients and HCs (Figure1b, red points). A PCA depicting 39 DEPs is shown in Figure1c. Hierarchical clustering of the 39 DEPs demonstrate that there are clear differences between NMOSD patients and HCs (Figure1d).
To help determine whether the DEPs are specific to NMOSD or demyelinating disease in general, we collected serum from an additional 12 patients with MS. Among the cytokines examined, the expression levels of 12 cytokines differed between MS patients and HCs (Figure2a). The PCA of all the 12 DEPs are shown in Figure 2B. Hierarchical clustering of these 12 proteins illustrate a difference between MS and HCs (Figure2c).
Functional profiling of the NMOSD-specific predictors.
Interestingly, 29 DEPs were NMOSD-specific (Figure3a, green box) and 2 proteins were MS-specific (Figure3a). After filtering multicollinear variances, the AUCs of 20 NMOSD-specific proteins were > 0.65 (Figure3b). To estimate the discrimination accuracy of the NMOSD-specific proteins, three supervised models (RDA, SVM, GBM) for 5 proteins were conducted to classify NMOSD patients from HCs. The GBM and SVM models distinguished NMOSD patients from HCs with 100% accuracy, 100% sensitivity, and 100% specificity. The RDA model classified NMOSD patients and HCs with 86.67% accuracy, 88.24% sensitivity, and 85.37% specificity (Figure3c). The protein concentrations of growth-regulated alpha protein (GRO), EGF, and TNF superfamily member 14 (LIGHT) in NMOSD patients and HCs are shown in Figure 3d.
There were 10 DEPs in both NMOSD and MS conditions compared to HCs, which include IL-17B, brain-derived neurotrophic factor (BDNF), IL-18 BPa, Angiopoietin-1 (ANG-1), Eotaxin-2, thymus and activation-regulated chemokine (TARC), GCP-2, CD40L, CD14, and Opsin-5 (OPN) (Figure 3a, blue box, inset). These proteins had an up/up or down/down trend, respectively, which indicates that a more general mechanism of the inflammatory demyelinating disease likely exists.
Differentially co-expressed modules between NMOSD and MS
Changes in protein levels provide a binary view of NMOSD (i.e., levels significantly change or not). However, disease is a gradual process as a patient’s optic nerve, spinal cord, or motor disability become increasingly impaired or affected. Therefore, the differential co-expression was analyzed to identify functional modules that may be significantly associated with the measured clinical traits.
A total of 9 differentially co-expressed protein modules were identified, with each module assigned a specific color in Figure 4a. Seven (7) distinct clusters of module proteins with highly similar or different correlation profiles between NMOSD and MS conditions are indicated as “a-g” in Figure 4a. The brown and magenta modules were significantly and highly correlated with each other in patients with MS compared to patients with NMOSD. The functions of the proteins in the brown module are related to the MAPK signaling pathway. Notably, the expression levels of these proteins are significantly different in the serum of MS and NMOSD patients, thus reflecting different disease pathologies.
Next, the correlations between co-expressed protein modules and clinical traits were determined. The blue module was moderately and positively associated with Erythrocyte Sedimentation Rate (ESR) (r=0.47, p=4e-07). The blue (r=0.43, p=0.002 and r=0.4, p-0.003) and pink (r=0.41, p=0.003 and r=0.44, p=0.001) modules were moderately and positively associated with cholesterol (CHOL) and low-density lipoprotein (LDL). The turquoise module was moderately and negatively associated with total protein (TP) (r=-0.51, p=1e-04), globulin (GLB) (r=-0.4, p=0.003), and adenosine deaminase (ADA) (r=-0.46, p=7e-04).
The correlations between 30 proteins (i.e., 29 NMOSD-specific proteins and IL-6R) and clinical traits were explored. Both a circos plot and a heatmap showed protein-trait associations (Figure 4b - c). Vascular endothelial growth factor C (VEGF-C) (r=0.52, p=0.003), myeloid progenitor inhibitory factor 1 (MPIF-1) (r=0.54, p=0.002), and neuronal cell adhesion molecule (NrCAM) (r=0.53, p=0.003) were positively associated with AQP-4-IgG titer. EGF was positively associated with ESR (r= 0.57, p=0.001). Mast/stem cell growth factor receptor kit (SCF R) and IL-6R were positively associated with serum amylase (AMS) (r= 0.58, p=8e-04 and r=0.54, p=0.002, respectively).
Serum cytokine profile analysis based on presence of AQP-4-IgG
Next, we sought to determine whether the presence of AQP-4-IgG in serum had distinct cytokine characteristics within the NMOSD cohort. When the serum proteins were analyzed based on the presence or absence of AQP-4-IgG, 15 proteins (p < 0.05 and absolute log2 FC > 0.263) differed between AQP-4+ and AQP-4- NMOSD patients (Figure 5a, red points). The PCA of all 15 DEPs are shown in Figure 5b. Clustering of the 15 different proteins illustrated clear differences between AQP-4+ and AQP-4- NMOSD patients (Figure 5c). Meanwhile, only 2 cytokines (IL-29, MPIF-1) differed between HCs and NMOSD patients (data not shown). Importantly, 9 cytokines (p < 0.05 and absolute log2 FC> 0.263) differed between AQP-4-IgG seronegative NMOSD and MS patients (Figure 5d). The PCA of the 9 DEPs are shown in Figure 5e. Hierarchical clustering of the 9 DEPs illustrate clear differences between the two groups (Figure 5f). Interestingly, the expression of GCP-2 and CD14 not only differed between AQP-4+ and AQP-4- NMOSD patients, but also differed between AQP-4- NMOSD and MS patients (Figure 5g).