The impact of Yiwei decoction on the LncRNA and CircRNA regulatory networks in premature ovarian insufficiency

Abstract

Premature ovarian insufficiency（POI）is a female reproductive aging illness. Yiwei decoction（YWD） is a traditional treatment for Yangming nourishment. YWD can treat premature ovarian insufficiency, but the exact molecular mechanism is unknown. As a result, the differential expression of Long noncoding RNAs (LncRNAs) and Circular RNAs(CircRNAs) in the ovary of POI rats after YWD treatment was investigated in this paper, and the CeRNA regulatory network was built. The model was created using cyclophosphamide. The model group + YWD was in Group A, the model control group was in Group B, and the regular control group was in Group C. In this study, 177 differential expression Long noncoding RNAs(DELncRNAs) and 190 differential expression Circular RNAs (DECircRNAs) were discovered between A and B (P＜0.05,|LogFC|＞1). Following the analysis, 27 DELncRNAs and 96 DECircRNAs (P-adjusted＜0.05,|LogFC|＞1) were discovered. At the same time, we built the CeRNA network using differentially expressed mRNAs and microRNAs (miRNAs) expression between groups A and B. The DELncRNAs were used to construct a lncRNA-miRNA-mRNA ceRNA network with 27 LncRNAs, 4 miRNAs, and 19 mRNAs. The DECircRNAs were utilized to establish a CircRNA-miRNA-mRNA ceRNA network that was made up of 15 CircRNAs, 4 miRNAs, and 20 mRNA. The highly correlated regulatory networks were the LncMSTRG.22691.3/miR-3102/ANGPT4 and Circ10_34698898_34699378/miR-33-5p/TTC22. Circ20_12035276_12036793、Circ20_30693935_30696337、Circ4_157723097_157723378 and Circ4_157923266_157923904 occurred concurrently in AvsB, BvsC, and AvsC. MiRDB predicted eight target miRNAs for these CircRNAs. The miRanda(score = 140，energy = -1) binding energy calculation revealed that seven miRNAs were well combined with three CircRNA base complementary pairs. This implies that 3 DECircRNAs could serve as spongy bodies for these miRNAs. Network pharmacological analysis showed that ten active components in YWD may regulate the expression of LncRNAs and CircRNAs, such as Stigmasterol, Uridine, Ophiopogonanone A, Gamma-Aminobutyric Acid, and others. In conclusion, this study combined transcriptomics and network pharmacological analysis to identify differentially expressed lncRNAs as well as CircRNAs in ovaries of YWD-treated POI rats, thereby constructing ceRNA networks implicated in POI. This would contribute to clarifying the pathways by which Chinese herbal compounds regulate gene expression in POI.

Keywords: CeRNA; Non-coding RNA; Premature ovarian insufficiency; Traditional Chinese medicine; Transcriptomics.

Fig. 1

The expression patterns of DELncRNAs and DECircRNAs in comparisons of AvsB, BvsC, and AvsC. Light blue dots represent downgrades, while light orange dots represent upgrades. DELncRNA group comparisons are represented by A, B, and C, while DECircRNA group comparisons are represented by D, E, and F. Each graphic includes annotated comparisons between groups. A, B, and C in the diagram indicate the three groupings. The p-value means the significance of the difference between the two groups. Fold Change represents the fold difference in gene expression between the two groups. DELncRNAs and DECircRNAs are labeled in the figure because they appear in all three sets of differential expression comparisons.

Fig. 2

Rectangular heat maps were used to display 45 DELncRNAs with P-adjust＜0.05. Red represents high expression, while blue represents low expression. A, B, and C in the diagram indicate the three groupings. The lines on the left and top of the image show the cluster analysis results between the nine samples and Lncrnas.

Fig. 3

A ring heat map was used to display 190 DECircRNAs that met P-adjust＜0.05. Red represents high expression, while blue represents low expression. A, B, and C indicate the mean expression of samples from the three groups. The black wire lines in the circular image show the findings of the CircRNA cluster analysis.

Fig. 4

In the CeRNA network of LncRNA-miRNA-mRNA, blue represents miRNAs, red represents mRNAs, and purple represents LncRNAs. The thickness and color of the connection lines between nodes represent the connection's P value. The green connection line indicates a negative correlation, while the red line indicates a positive correlation.

Fig. 5

Blue represents miRNAs, red represents mRNAs, and green represents CircRNAs in the CeRNA network CircRNA-miRNA-mRNA. The wiring is identical to that shown in Fig. 4.

Fig. 6

A represents DECircRNAs at the intersection of AvsB, BvsC, and AvsC. B, C, and D represent the binding sites of CircRNAs and miRNAs, respectively. The green rings in B, C, and D represent CircRNAs, and the inner blue rectangles are miRNAs. The length of the CircRNA base sequence is shown by the number in the green ring superscript.

Fig. 7

The precise location of CircRNAs binding to miRNAs and the details of base complementarity are depicted. "|" represents the hydrogen bond, ":" means the two hydrogen bonds and energy represents the energy required for base pairing. Red represents sequences with complementary bases.

Fig. 8

TCM-active ingredients-target-ncRNAs: TCM is represented by orange; The color green represents the active ingredient; The intersection of the YWD target and the host gene of ncRNA is represented in blue; The light red represents CircRNAs; LncRNAs are represented by purple.