Clinical characteristics of the subjects after PSM
Of the 220 subjects who participated in the study, clinical data and specimens were collected from 198. After the withdrawal of 15 subjects, a total of 183 completed full ophthalmologic examinations. The mean age of the subjects was 66.8 yrs, mean T2DM duration was 22.6 yrs, and 50.3% were female. Of a total of 183 subjects who underwent ophthalmologic examinations, 124 (67.8%) were diagnosed with DR; and 46 (25.1%) were diagnosed with DME. PSM was performed, and 30 pairs of cases and controls with no significant differences in terms of clinical characteristics, except for the presence or absence of DME, were selected (Table S1). In addition, validation of the results derived from the discovery set was performed using a validation set of 43 pairs.
Discovering multi-biomarkers of DME in plasma
Based on metabolomics studies, we sought to discover multi-biomarkers in plasma which can help diagnose DME among DM subjects. A schematic diagram of the experimental processes involved is summarized in Figure 1. First, we performed non-targeted metabolite and oxylipin profiling in the discovery cohort. Metabolites distinguishing subjects with and without DME were identified and selected as candidate metabolite biomarkers. The candidate metabolite biomarkers were confirmed in the extended cohort by comparing relative levels. Multi-biomarkers for discriminating DME and non-DME subjects were finally selected with the following qualifications: 1. Statistically significant discriminating metabolites from both the discovery and extended cohorts. 2. Metabolites exhibiting good discriminatory power for DME versus non-DME subjects, with an area under the curve (AUC) > 0.7.
GC-TOF-MS analysis-based metabolite profiling and oxylipin analysis in plasma
GC-TOF-MS analysis-based metabolite profiling was performed using plasma from discovery cohort subjects and multivariate statistical analysis (Figure 2). In PCA score plots derived from metabolite profiling data sets using GC-TOF-MS analysis, the groups of DME and non-DME subjects were not clearly separated from each other. However, in the partial least squares–discriminant analysis (PLS-DA) model with supervised methods, these two groups were clearly distinguished from each other along with PLS1 (8.2%). The quality of the PLS-DA model was evaluated by R2Y(cum) = 0.847, Q2(cum) = 0.546, and by cross-validation analysis (7.77e-7), which signify a valid model. To select the metabolites responsible for the group separation, VIP values > 0.7 of PLS-DA were applied. A total of 49 metabolites, including 19 amino acids, 14 organic compounds, 8 fatty acids and lipids, and 8 carbohydrates were identified as metabolites that differed between the DME and non-DME groups of subjects. In addition, a total of 60 oxylipins were identified by targeted analysis. Those included 36 arachidonic acid-, 9 DHA-, 6 EPA-, and 9 linoleic acid-derived oxylipins. The relative metabolite levels were normalized to average values and visualized with heat maps (Figure S2A)
Validation of plasma metabolite biomarkers for discriminating DME from non-DME cases
To validate plasma metabolite biomarkers derived from the discovery cohort, we further performed multivariate analysis and oxylipin profiling using the extended cohort. The PCA and orthogonal PLS-DA (OPLS-DA) score plots revealed similar tendencies to those of the discovery cohort (Figure S1). However, the OPLS-DA model values were R2Y(cum) = 0.693 and Q2(cum) = 0.211, which indicated that the fitness and prediction accuracy of the model was lower than observed for the discovery cohort. The quality of the model was evaluated by cross-validation analysis (p-value = 0.0009). Metabolites distinguishing DME from non-DME subjects were selected according to the VIP value (> 0.7) of the extended cohort, and relative levels were visualized using heat maps (Figure S2B). By comparison of heat maps derived from the discovery and extended cohorts, relative metabolite levels between the groups of patients with DME and non-DME revealed similar tendencies. Multi-biomarkers for diagnosing DME patients were finally selected the following qualifications: 1. Statistically significant discriminant metabolites from both the discovery and extended cohorts. 2. Metabolites showing good discriminatory power for DME versus non-DME subjects, with an AUC > 0.7. Among the assigned metabolites, glutamic acid, cysteine, asparagine, aspartic acid, lysine, uric acid, malic acid, citric acid, nonanoic acid, 15-oxoETE, 12-oxoETE, 20-carboxy leukotriene B4, and 9-oxoODE exhibited statistically significant different levels between the groups of subjects with DME and non-DME in both the discovery and extended cohorts (Table S2-S5). ROC curves were also generated for the 109 assigned metabolites using the relative metabolite levels of the experimental group in the discovery cohort (Table S2 and S3). Among them, metabolites which exhibited good discriminatory power for diabetic versus DME cases with an AUC > 0.7 included glutamic acid (0.762), cysteine (0.733), asparagine (0.772), aspartic acid (0.715), lysine (0.726), uric acid (0.786), citric acid (0.796), phenylacetic acid (0.810), 15-keto prostaglandin F2α (0.750), 15-keto prostaglandin E2 (0.719), 15-oxoETE (0.812), 12-oxoETE (0.867), 20-carboxy leukotriene B4 (0.743), 9-oxoODE (0.755), and (±) 9-HODE or (±) 13-HODE (0.743). Finally, multi-biomarkers selected for distinguishing DME patients from non-DME subjects for diagnosis were asparagine (0.729-fold change), aspartic acid (0.782-fold), glutamic acid (0.653-fold), cysteine (0.666-fold), lysine (0.849-fold), citric acid (0.741-fold), uric acid (0.707-fold), 12-oxoETE (1.526-fold), 15-oxoETE (1.319-fold), 9-oxoODE (0.692-fold), and 20-carboxy leukotriene B4 (5.575-fold). A combination of these metabolites from GC-TOF-MS-based metabolite profiling, including asparagine, aspartic acid, glutamic acid, cysteine, lysine, citric acid, and uric acid, greatly improved the specificity of distinguishing DME subjects from non-DME cases, with a combined AUC value of 0.918 (Figure 3). In addition, a combination of oxylipins, including 12-oxoETE, 15-oxoETE, 9-oxoODE, and 20-carboxy leukotriene B4, yielded a combined AUC value of 0.957, also demonstrating improved power in discriminating DME and non-DME subjects (Figure 3).
Differences in metabolism according to generation of DME
From plasma metabolome analysis of subjects with and without DME, various metabolites were selected as discriminatory factors, and we constructed a metabolic pathway to illustrate the relationships between metabolism and generation of DME (Figure 4). In the pathway, carbohydrates, phenylalanine, alanine, aspartate, glutamate, arginine, and oxylipin metabolism (linoleate, eicosapentanoate, arachidonate and, docosahexaenoate metabolism) exhibited differences distinguishing patients with and without DME. In particular, metabolites such as serine, threonine, alanine, aspartate, and glutamate, and the tricarboxylic acid (TCA) metabolic cycle, were significantly decreased in subjects with DME compared with that in non-DME subjects. In the case of oxylipin metabolism, relative metabolite levels of oxylipin precursor fatty acids, such as linoleic, eicosapentanoic, arachidonic, and docosahexaenoic acids, were not significantly different between DME and non-DME subjects. However, the relative amounts of oxylipins produced from different precursor fatty acids did exhibit significant differences. Among them, most oxylipins involved in linoleate, EPA, and DHA metabolism showed relatively low metabolite levels in subjects with DME compared with that in non-DME subjects. In particular, in linoleate metabolism, oxylipins generated by lipoxygenase, peroxidase, and dehydrogenases such as (±) 9-HODE or (±) 13-HODE and 9-oxoODE were present at significantly lower levels in subjects with DME than in those without DME. In the case of arachidonate metabolism, a variety of oxylipins displayed increased and decreased metabolism due to DME compared those in non-DME subjects. Among these, levels of 20-carboxyleukotriene B4, 12-oxoETE, and 15-oxoETE, which are catalyzed by various enzymes, including hydroxylase, carboxylase, lipoxygenase, peroxidase, and dehydrogenase, were significantly elevated in DME subjects compared with those in non-DME subjects. On the other hand, 15-keto prostaglandin F2α, which is also generated by dehydrogenase activity, exhibited significantly decreased levels in subjects with DME.