3.1. Identification of Significantly Regulated Metabolites
Preprocessing of the raw data revealed a total of 126 metabolites peaks as shown in Table S1. Unsupervised PCA showed the clustering and almost total separation of the treatment and control group with no outlier present (Figure 1A). Figure 1B shows the supervised fitted model of OPLS-DA and it can be seen that the separation of the two groups was much more distinct with an R2X, R2Y and Q2 of 0.332, 0.977 and 0.590, respectively, indicating the model has good predictability[18]. After 200 permutations, the R2Y and Q2 values were generally lower than that of the original model and the Q2 intercept value was < 0 at (0, -0.69) (Figure 1C). These showed that there was no overfitting for the OPLS-DA model[20, 21]. Based on the criteria of t-test P value < 0.05 and VIP > 1[20, 21], 6 significantly up-regulated and 11 significantly down-regulated metabolites were identified (Figure 1D and Table 1). Hierarchical clustering of the 17 significantly regulated metabolites further validated the specific up- or downregulatory effects of GCNY in the treatment group as compared to the control group (Figure 2A).
Figure 1: Multivariate analyses of metabolite signatures and identification of significantly regulated metabolites. (A) PCA score scatter plot of metabolite profiles in control mice and mice treated with GCNY. Each point represents a metabolite profile of a biological replicate. All points fall within the Hotelling’s T2 ellipse (95% confidence interval). PC[1] and PC[2]: principal component 1 and 2. (B) OPLS-DA score scatter plot of metabolite profiles in control mice and mice treated with GCNY. R2X, R2Y and Q2 were 0.332, 0.977 and 0.590, respectively. Each point represents a metabolite profile of a biological replicate. All points fall within the Hotelling’s T2 ellipse (95% confidence interval). t[1]P: predicted principal component score of the first principal component; t[2]O: orthogonal principal component score. (C) Validation of the OPLS-DA model using permutation test of 200 random permutations. Intercepts of R2Y and Q2 were (0, 0.9) and (0, -0.69), respectively. (D) Volcano plot identifying significantly regulated metabolites associated to GCNY treatment. A threshold of P = 0.05 (-log10P-value = 1.3) was used.
Table 1: Significantly regulated metabolites associated to GCNY treatment.
Metabolite
|
Retention time (s)a
|
HMDB
|
Direction of regulation
|
Thiamine
|
625.69
|
HMDB00235
|
Down
|
gamma-L-Glutamyl-L-valine
|
719.42
|
HMDB11172
|
Down
|
Pantothenic acid
|
503.88
|
HMDB00210
|
Down
|
Pyridoxal (Vitamin B6)
|
175.65
|
HMDB01545
|
Down
|
Succinic acid
|
742.40
|
HMDB00254
|
Down
|
Uridine 5'-diphospho-glucuronic acid (UDP-D-Glucuronate)
|
913.63
|
HMDB00935
|
Down
|
Uridine
|
282.02
|
HMDB00296
|
Down
|
Isobutyrylglycine
|
394.00
|
HMDB00730
|
Up
|
Allantoic acid
|
672.44
|
HMDB01209
|
Down
|
N-Acetylcadaverine
|
541.66
|
HMDB02284
|
Up
|
N-Acetyl-D-glucosamine
|
465.88
|
HMDB00215
|
Down
|
N-Carbamoyl-L-aspartic acid
|
805.11
|
HMDB00828
|
Up
|
Nicotinamide ribotide
|
884.74
|
HMDB00229
|
Down
|
N2,N2-Dimethylguanosine
|
338.43
|
HMDB04824
|
Down
|
L-Anserine
|
782.04
|
HMDB00194
|
Up
|
Creatinine
|
294.17
|
HMDB00562
|
Up
|
cis-4-Hydroxy-D-proline
|
665.11
|
HMDB60460
|
Up
|
a: median retention time; HMDB: Human Metabolome Database
3.2. Correlation Analysis of the Significantly Regulated Metabolites
Figure 2B shows the correlation analysis results of the 17 significant metabolites. A positive correlation was observed between metabolites regulated in the same direction whereas an inverse correlation was always observed between metabolites regulated in opposite directions. Among the up-regulated metabolites, creatinine was positively correlated to both N-carbamoyl-L-aspartic acid and L-anserine (r = 0.631, P = 0.028 and r = 0.810, P = 0.001, respectively) whereas L-anserine was positively correlated to N-carbamoyl-L-aspartic acid (r = 0.720, P = 0.008). On the other hand, notable very strong positive correlation (r > 0.8) among the down-regulated metabolites include gamma-L-Glutamyl-L-valine and UDP-D-Glucuronate (r = 0.859, P < 0.001), pantothenic acid and uridine (r = 0.835, P = 0.001) , pantothenic acid and UDP-D-Glucuronate (r = 0.837, P = 0.001), pantothenic acid and gamma-L-glutamyl-L-valine (r = 0.969, P < 0.001), succinic acid and nicotinamide ribotide (r = 0.835, P = 0.001) and L-anserine and creatinine (r = 0.810, P = 0.040). There was only one very strong negative correlation (r < -0.8) observed for L-anserine and thiamine (r = -0.837, P = 0.001) (Figure 2B).
Figure 2: Analysis of significantly regulated metabolites. (A) Hierarchical clustering analysis for control mice and GCNY-treated mice. (B) Correlation analysis for control mice and GCNY-treated mice. The upper triangle denotes the Pearson’s r whereas the lower triangle denotes the respective P values. Significant Pearson’s r and P values are bolded.
3.3. Metabolic Pathway and Integrated Network Analysis
Utilizing HMDB, Pubchem and KEGG, all the pathways involving the significantly regulated metabolites were identified and are shown in Figure S1. Among these pathways, 11 metabolic pathways were associated with treatment using GCNY (Figure 3 and Table 2) with a high correlation. A combined consideration of the P and impact value revealed that 6 pathways were significantly altered: 1) alanine, aspartate and glutamate metabolism, 2) pyrimidine metabolism, 3) thiamine metabolism, 4) amino sugar and nucleotide sugar metabolism, 5) pantothenate and CoA biosynthesis and 6) citrate cycle (TCA cycle). Figure 4 shows an integrated metabolic network that connects 4 of the 6 significantly altered pathways (pantothenate and CoA biosynthesis, pyrimidine metabolism, alanine, aspartate and glutamate metabolism and TCA cycle). Three metabolites: pantothenate, succinate and uridine were found to be down-regulated (fold change of 0.40, 0.53 and 0.64, respectively) following GCNY treatment whereas only N-carbomoyl-L-aspartate, which was involved in both the alanine, aspartate and glutamate metabolism and pyrimidine metabolism pathways, was found to be significantly up-regulated with a fold change of 2.72.
Table 2: Metabolic pathways associated to GCNY treatment. Significantly altered pathways are bolded.
Pathway
|
Totala
|
Hitsb
|
P
value
|
Holm Pc
|
Impact value
|
Alanine, aspartate and glutamate metabolism
|
24
|
2
|
0.011
|
0.934
|
0.000
|
Pyrimidine metabolism
|
41
|
2
|
0.032
|
1.000
|
0.035
|
Thiamine metabolism
|
7
|
1
|
0.048
|
1.000
|
0.400
|
Nicotinate and nicotinamide metabolism
|
13
|
1
|
0.088
|
1.000
|
0.000
|
Pantothenate and CoA biosynthesis
|
15
|
1
|
0.101
|
1.000
|
0.020
|
beta-Alanine metabolism
|
17
|
1
|
0.114
|
1.000
|
0.000
|
Propanoate metabolism
|
20
|
1
|
0.133
|
1.000
|
0.000
|
Citrate cycle (TCA cycle)
|
20
|
1
|
0.133
|
1.000
|
0.026
|
Butanoate metabolism
|
22
|
1
|
0.145
|
1.000
|
0.000
|
Amino sugar and nucleotide sugar metabolism
|
37
|
1
|
0.233
|
1.000
|
0.069
|
Purine metabolism
|
68
|
1
|
0.389
|
1.000
|
0.000
|
a: Total metabolites in the pathway; b: Number of significantly regulated metabolites in the pathway; c: Holm-Bonferroni corrected P values for multiple comparisons
Figure 3: The metabolome view map of significantly altered pathways related to treatment with GCNY. The x-axis represents the impact value in topology analysis whereas the y-axis represents the P value in enrichment analysis. Significantly altered pathways are labeled.