Construction and analysis of lncRNA-related ceRNA network in mouse model of methotrexate-induced neural tube defect under folate deficiency

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Construction and analysis of lncRNA-related ceRNA network in mouse model of methotrexate-induced neural tube defect under folate deficiency

Neurosciences | 更新时间：2026-01-09

- Construction and analysis of lncRNA-related ceRNA network in mouse model of methotrexate-induced neural tube defect under folate deficiency
- Journal of Army Medical University Vol. 45, Issue 1, Pages: 1-9(2023)
- 作者机构：
  
  1.100020 北京，首都儿科研究所，北京市儿童发育组学重点实验室
  2.100020 北京，北京协和医学院研究生院
- 作者简介：
- 基金信息：
  
  the General Program of National Natural Science Foundation of China(82071690);the Funds of Capital Institute of Pediatrics(FX-2020-05);the Funds of Capital Institute of Pediatrics(CXYJ-2-21-09)
- DOI：10.16016/j.2097-0927.202203181
  CLC： R394.1;R591.424;R742.89
- Received：21 March 2022，
  
  Revised：2022-08-07，
  
  Published：15 January 2023
- 稿件说明：
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Yubing ZENG, Fan LIU, Pei PEI, et al. Construction and analysis of lncRNA-related ceRNA network in mouse model of methotrexate-induced neural tube defect under folate deficiency[J]. Journal of Army Medical University, 2023, 45(1): 1-9.
DOI：

Yubing ZENG, Fan LIU, Pei PEI, et al. Construction and analysis of lncRNA-related ceRNA network in mouse model of methotrexate-induced neural tube defect under folate deficiency[J]. Journal of Army Medical University, 2023, 45(1): 1-9. DOI： 10.16016/j.2097-0927.202203181.

摘要

目的

2

构建低叶酸联合甲氨蝶呤(methotrexate，MTX)诱导神经管畸形(neural tube defect，NTDs)的胎鼠模型中lncRNA相关的竞争性内源RNA(competing endogenous RNAs，ceRNA)调控网络，探讨低叶酸条件下NTDs中lncRNA可能的调控作用。

方法

2

利用SPF级、7~8周龄的健康雌性C57BL/6J小鼠(体质量18~22 g)40只及健康雄性C57BL/6J小鼠(体质量20~22 g)20只，建立叶酸缺乏情况下的NTDs胎鼠模型为实验组，并设立对照组，每组选取3只胎鼠分离脑组织并提取总RNA，进行高通量RNA测序(RNA sequencing

RNA-seq)，并对测序结果进行lncRNA-mRNA共表达网络构建、对共表达网络中mRNA进行GO功能富集及KEGG通路富集分析、构建lncRNA相关ceRNA调控网络，并用qPCR验证胎鼠、细胞样本中lncRNA Xist、Sema4f、Padi2的相对表达量。

结果

2

测序共检测到差异lncRNA 47个(Log

2

FC＞0.585或Log

2

FC＜-0.585，FDR

<

0.05)，其中上调38个，下调9个。构建lncRNA和mRNA基因间的共表达网络，并对共表达网络关系中的mRNA进行KEGG/GO功能富集分析，发现GO条目中管道发育(

P

<

0.001)、胶原蛋白代谢过程(

P

=0.002)、系统发育(

P

=0.002)等显著富集，在KEGG通路分析中富集到与NTDs密切相关的PI3K-Akt通路；构建lncRNA相关ceRNA调控网络，发现lncRNA Xist、LOC102633899、1700086L19Rik等靶向差异基因Sema4f、Padi2、Lin28a等；选取与神经发育密切相关的lncRNA Xist及预测的靶基因Sema4f、Padi2，用qPCR验证胎鼠脑组织、细胞样本，结果与测序一致，相较对照组，均显著下调(

P

<

0.05)。

结论

2

在叶酸缺乏下的NTDs胎鼠模型中lncRNA Xist及预测的靶基因Sema4f、Padi2发生显著下调。

Abstract

Objective

2

To construct a regulatory network of long noncoding RNA (lncRNA)-related competing endogenous RNAs (ceRNA) in low folate combined with methotrexate (MTX) induced neural tube defects (NTDs) mouse model

and to explore the potential lncRNAs regulation in low folate-induced NTDs.

Methods

2

Forty SPF-grade 7~8-week-old healthy female C57BL/6J mice (body weight 18~22 g) and 20 healthy male C57BL/6J mice (20~22 g) were selected to this experiment. After a folate deficiency induced fetal mouse NTD model was successfully established

the embryonic brain tissues were extracted for total RNA and RNA high-throughput sequencing (RNA-seq) was performed. The results of RNA-seq were used to carry out co-expression network construction

GO function enrichment of mRNA in co-expression network and KEGG pathway enrichment analysis

construction of lncRNA-related ceRNA regulation network and other bioinformatics analysis. And the relative expression of lncRNA Xist

Sema4f and Padi2 in the fetal mouse and cell samples was verified by qPCR.

Results

2

A total of 47 differential lncRNAs (Log

2

FC

>

0.585 or Log

2

FC

<

-0.585

FDR

<

0.05) were detected by RNA-seq

of which 38 were up-regulated and 9 were down-regulated. The co-expression network between lncRNA and mRNA was constructed. The results of KEGG/GO analysis on mRNAs in the co-expression network indicated that tube development (

P

<

0.001)

collagen metabolic process (

P

=0.002)

system development (

P

=0.002) and other significant enrichments were highly relevant to NTDs. Besides

KEGG pathway analysis displayed that the PI3K-Akt pathway was closely related to NTDs; lncRNA Xist

LOC102633899

1700086L19Rik and other targeting differential genes Sema4f

Padi2

Lin28a were found in the lncRNA-related ceRNA network. qPCR confirmed that the above results in the fetal mice and cell samples under folic acid

deficiency

with consistent corresponding sequences

and obviously down-regulated (

P

<

0.05).

Conclusion

2

In folic acid deficiency-induced mouse NTD model

lncRNA Xist

and its targeting genes Sema4f and Padi2 are obviously down-regulated.

关键词

Keywords

references

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