NOTES
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CONFLICTS OF INTEREST
No potential conflict of interest relevant to this article was reported.
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AUTHOR CONTRIBUTIONS
Conception or design: Y.L., C.Q.C., Y.L.
Acquisition, analysis, or interpretation of data: Y.L., Y.Z., M.Z., J.Z., Y.Z., X.Y.
Drafting the work or revising: Y.L., Q.L., H.C., C.Q.C., Y.L.
Final approval of the manuscript: Y.L., Y.Z., M.Z., J.Z., Y.Z., X.Y., Q.L., H.C., C.Q.C., Y.L.
Supplementary Fig. 2
Gel electrophoresis analysis of quantitative real-time polymerase chain reaction (qRT-PCR) products. To demonstrate qRT-PCR specificity, we performed agarose gel electrophoresis using qRT-PCR products. All the circular RNA (circRNA) PCR products showed a single band, demonstrating high specificity and reliability of qRT-PCR results.
dmj-2019-0151-s007.pdf
Supplementary Fig. 3
Detailed annotation of circular RNA (circRNA)/microRNA (miRNA) interaction for hsa_circRNA_101062 and hsa_circRNA_100332. For each circRNA, five predicted miRNA response elements are included: (A) hsa_circRNA_101062, (B) hsa_circRNA_100332.
dmj-2019-0151-s008.pdf
Supplementary Fig. 4
Detailed annotation of circular RNA (circRNA)/microRNA (miRNA) interaction for hsa_circRNA_085129 and hsa_circRNA_103845. For each circRNA, five predicted miRNA response elements are included: (A) hsa_circRNA_085129, (B) hsa_circRNA_103845.
dmj-2019-0151-s009.pdf
Fig. 1Overview of differentially expressed plasma circular RNAs (circRNAs) identified in patients with newly diagnosed type 1 diabetes mellitus (T1DM) by microarray. (A) The box plot shows intensity distribution of expressed circRNA across all the samples after normalization. The central line within each box represents the median of the data, whereas the error bars represent the upper and lower quartiles. (B) Volcano plots show differentially expressed plasma circRNAs with fold-change greater than 2 and P value less than 0.05 between control and T1DM subjects. The upwards and downwards arrows indicate up- and down-regulated circRNA clusters, respectively. (C) Hierarchical cluster analysis (heat map) for visualizing differentially expressed circRNAs, wherein red and green colors denote high and low expression levels, respectively. C1–C3, healthy controls; D1–D3, T1DM patients.
Fig. 2Classification of differentially expressed circular RNAs (circRNAs). (A) Genomic origins of differentially expressed circRNAs. (B) Chromosome distribution of differentially expressed circRNAs.
Fig. 3Verification of microarray data by quantitative real-time polymerase chain reaction. Using independent human samples, our results confirmed that hsa_circular RNA (circRNA)_085129 (A), hsa_circRNA_100332 (B), hsa_circRNA_101062 (C) and hsa_circRNA_103845 (D) were all upregulated in type 1 diabetes mellitus (T1DM). However, expression of hsa_circRNA_005178 (E) remained unchanged. circRNA, circular RNA. Data are expressed as fold-change over healthy controls and represented as the mean±standard error (n=12). NS, not significant. aStatistically significant difference (P<0.05), bStatistically significant difference (P<0.01).
Fig. 4The circular RNA (circRNA)-microRNA (miRNA)-messenger RNA (mRNA) network for the validated four circRNAs. Each circRNA interacts with its five miRNA response elements (MREs) and representative downstream mRNAs. For the convenience of visualization, only mRNAs with cumulative weighted context++ score no more than −0.7 were included. Specifically, hsa-miR-660-3p had the largest number of downstream target genes and hsa-miR-5189-5p exhibited the most interactions with other circRNA clusters. Red diamonds, circRNAs. Blue squares, miRNAs. Green ovals, mRNAs.
Fig. 5Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using predicted target messenger RNAs (mRNAs) of validated four circular RNA (circRNA). (A) GO enrichment analysis comprises three categories: biological process (in blue), cellular component (in green) and molecular function (in orange). Top five terms of each category are displayed. (B) KEGG pathway analysis shows top 10 terms that may be involved in the regulatory network mediated by differentially expressed circRNAs in type 1 diabetes mellitus.
Table 1.Characteristics and demographics of human participants
Characteristic |
Microarray screening
|
qRT-PCR validation
|
Control (n=3) |
T1DM (n=3) |
Control (n=12) |
T1DM (n=12) |
Age, yr |
16 (12–18) |
15 (12–17) |
12.6 (6–18) |
12.8 (5–17) |
Gender, female/male |
0/3 |
2/1 |
6/6 |
7/5 |
Disease duration, mo |
- |
3.7±2.1 |
- |
3.0±1.9 |
HbA1c, % |
5.6±0.1 |
9.7±0.8 |
5.4±0.4 |
9.9±1.2 |
Subjects positive for ≥1 islet Aba
|
0 |
3 |
0 |
12 |
Serum C-peptide during OGTT, ng/mLb
|
|
|
|
|
0 min |
- |
0.16±0.15 |
- |
0.19±0.18 |
60 min |
- |
0.21±0.18 |
- |
0.39±0.37 |
120 min |
- |
0.3±0.41 |
- |
0.54±0.38 |