Skip to main content
SpringerLink
Log in

Integrating lncRNAs and mRNAs expression profiles in terminal hindgut of fetal rats with anorectal malformations

  • Original Article
  • Published:
Pediatric Surgery International Aims and scope Submit manuscript

Abstract

Background

The detailed embryonic etiology and pathogenesis of anorectal malformations (ARMs) remains unclear. Recent studies have shown that gene expression abnormalities were the key factors that result in ARMs. Long non-coding RNAs (lncRNAs) were reported as the ‘transcriptional noise’ within the genome. The expression profiles of lncRNA and mRNA remain less characterized in the pathogenesis of ARMs. Furthermore, the function of lncRNAs in the regulation of this process has not been investigated so far. Therefore, this current study was aimed to integrate lncRNA and mRNA expression profiles in terminal hindgut of ethylenethiourea (ETU)-induced ARM rats using Agilents lncRNA and mRNA co-expression microarrays.

Methods

ARM model was induced with ethylenethiourea (ETU) on gestational day 10. Cesarean deliveries were conducted to collect the embryos on gestational day 20. For the extraction of total RNA, 1-cm terminal hindgut tissues were collected from three fetal rats with similair weights. The microarrays and quantitative RT-PCR analysis were conducted to evaluate the lncRNA and mRNA expression profiles in normal fetal rats and ARM fetal rats.

Results

Compared with control group, 164 lncRNAs were observed to be aberrantly expressed (FC ≥ 2; P < 0.05) in ARM group, including 36 upregulated and 128 downregulated, while 772 mRNAs were observed to be aberrantly expressed (FC ≥ 2; P < 0.05) in the terminal hindgut, including 350 up-regulated and 422 down-regulated. The differential expression profiles between the ARM and the control group were used for gene ontology (GO) and pathway analysis. A subset of those RNAs was identified to be closely related to the development process of ARMs. The four RNAs that were differentially expressed between the two groups were selected for qPCR validation, and the results were in line with the microarray data. In addition, the lncRNAs and mRNA co-expression network was established according to the correlation analysis. We predicted the functions of transregulatory lncRNAs by the TFs (transcription factors) which might modulate their expression. In the core network of lncRNA–TF pairs, the lncRNAs can be classified into 5 categories of pathways governed by Jun, c-Myc, Usf1, Alf2, and Stat3.

Conclusion

From the above results, it can be suggested that these aberrant lncRNAs might participate in the pathogenesis of ARM, and our present work may provide new research directions for future studies of ARMs.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  1. Herman RS, Teitelbaum DH (2012) Anorectal malformations. Clin Perinatol 39(2):403–422

    Article  PubMed  Google Scholar 

  2. Bai Y, Yuan Z, Wang W et al (2000) Quality of life for children with fecal incontinence after surgically corrected anorectal malformation. J Pediatr Surg 35(3):462–464

    Article  PubMed  CAS  Google Scholar 

  3. Levitt MA, Peña A (2005) Outcomes from the correction of anorectal malformations. Curr Opin Pediatr 17(3):394–401

    Article  PubMed  Google Scholar 

  4. Peña A, Guardino K, Levitt MA et al (1998) Bowel management for fecal incontinence in patients with anorectal malformations. J Pediatr Surg 33(1):133–137

    Article  PubMed  Google Scholar 

  5. Endo M, Hayashi A, Ishihara M et al (1999) Analysis of 1992 patients with anorectal malformations over the past two decades in Japan. Steering Committee of Japanese Study Group of Anorectal Anomalies. J Pediatr Surg 34(3):435–441

    Article  PubMed  CAS  Google Scholar 

  6. Wang C, Li L, Cheng W (2015) Anorectal malformation: the etiological factors. Pediatr Surg Int 31(9):795–804

    Article  PubMed  CAS  Google Scholar 

  7. Lee JT (2012) Epigenetic regulation by long noncoding RNAs. Science 338(6113):1435–1439

    Article  PubMed  CAS  Google Scholar 

  8. Liu H, Chen P, Jiang C et al (2016) Screening for the key lncRNA targets associated with metastasis of renal clear cell carcinoma. Medicine (Baltimore) 95(2):e2507

    Article  Google Scholar 

  9. Lan X, Yan J, Ren J et al (2016) A novel long noncoding RNA Lnc-HC binds hnRNPA2B1 to regulate expressions of Cyp7a1 and Abca1 in hepatocytic cholesterol metabolism. Hepatology 64(1):58–72

    Article  PubMed  CAS  Google Scholar 

  10. Wang K, Liu CY, Zhou LY et al (2015) APF lncRNA regulates autophagy and myocardial infarction by targeting miR-188-3p. Nat Commun 6:6779

    Article  PubMed  CAS  Google Scholar 

  11. Zhang Y, Tao Y, Li Y et al (2018) The regulatory network analysis of long noncoding RNAs in human colorectal cancer. Funct Integr Genom. https://doi.org/10.1007/s10142-017-0588-2

    Article  Google Scholar 

  12. Vausort M, Wagner DR, Devaux Y (2014) Long noncoding RNAs in patients with acute myocardial infarction. Circ Res 115(7):668–677

    Article  PubMed  CAS  Google Scholar 

  13. Cao WJ, Wu HL, He BS et al (2013) Analysis of long non-coding RNA expression profiles in gastric cancer. World J Gastroenterol 19(23):3658–3664

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  14. Han L, Zhang K, Shi Z et al (2012) LncRNA profile of glioblastoma reveals the potential role of lncRNAs in contributing to glioblastoma pathogenesis. Int J Oncol 40(6):2004–2012

    PubMed  CAS  Google Scholar 

  15. Marini KD, Payne BJ, Watkins DN et al (2011) Mechanisms of Hedgehog signaling in cancer. Growth Factors 29(6):221–234

    Article  PubMed  CAS  Google Scholar 

  16. Mo R, Kim JH, Zhang J et al (2001) Anorectal malformations caused by defects in sonic hedgehog signaling. Am J Pathol 159(2):765–774

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Carter TC, Kay DM, Browne ML et al (2013) Anorectal atresia and variants at predicted regulatory sites in candidate genes. Ann Hum Genet 77(1):31–46

    Article  PubMed  CAS  Google Scholar 

  18. Garcia-Barceló MM, Chi-Hang Lui V, Miao X et al (2008) Mutational analysis of SHH and GLI3 in anorectal malformations. Birth Defects Res A Clin Mol Teratol 82(9):644–648

    Article  PubMed  CAS  Google Scholar 

  19. Zhang J, Zhang ZB, Gao H et al (2009) Down-regulation of SHH/BMP4 signalling in human anorectal malformations. J Int Med Res 37(6):1842–1850

    Article  PubMed  CAS  Google Scholar 

  20. Huang Y, Zhang P, Zheng S et al (2014) Hypermethylation of SHH in the pathogenesis of congenital anorectal malformations. J Pediatr Surg 49(9):1400–1404

    Article  PubMed  Google Scholar 

  21. Jia H, Chen Q, Zhang T et al (2011) Wnt5a expression in the hindgut of fetal rats with chemically induced anorectal malformations—studies in the ETU rat model. Int J Colorectal Dis 26(4):493–499

    Article  PubMed  Google Scholar 

  22. Guo C, Sun Y, Guo C et al (2014) Dkk1 in the peri-cloaca mesenchyme regulates formation of anorectal and genitourinary tracts. Dev Biol 385(1):41–51

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Geng Y, Mi J, Gao H et al (2017) Spatiotemporal expression of Wnt3a during striated muscle complex development in rat embryos with ethylenethiourea-induced anorectal malformations. Mol Med Rep 15(4):1601–1606

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  24. Ng RC, Matsumaru D, Ho AS et al (2014) Dysregulation of Wnt inhibitory factor 1 (Wif1) expression resulted in aberrant Wnt-beta-catenin signaling and cell death of the cloaca endoderm, and anorectal malformations. Cell Death Differ 21(6):978–989

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  25. Wong EH, Ng CL, Lui VC et al (2013) Gene network analysis of candidate loci for human anorectal malformations. PLoS One 8(8):e69142

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Brafman D, Willert K (2017) Wnt/beta-catenin signaling during early vertebrate neural development. Dev Neurobiol 77(11):1239–1259

    Article  PubMed  Google Scholar 

  27. Khanna K, Sharma S, Pabalan N et al (2018) A review of genetic factors contributing to the etiopathogenesis of anorectal malformations. Pediatr Surg Int 34(1):9–20

    Article  PubMed  Google Scholar 

  28. Camon E, Magrane M, Barrell D et al (2004) The gene ontology annotation (GOA) database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res 32(Database issue):D262–D266

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Du J, Li M, Yuan Z et al (2016) A decision analysis model for KEGG pathway analysis. BMC Bioinform 17(1):407

    Article  Google Scholar 

  30. Ma H, Hao Y, Dong X et al (2012) Molecular mechanisms and function prediction of long noncoding RNA. Sci World J 2012:541786

    Google Scholar 

  31. Kim ED, Sung S (2012) Long noncoding RNA: unveiling hidden layer of gene regulatory networks. Trends Plant Sci 17(1):16–21

    Article  PubMed  CAS  Google Scholar 

  32. De Lucia F, Dean C (2011) Long non-coding RNAs and chromatin regulation. Curr Opin Plant Biol 14(2):168–173

    Article  PubMed  CAS  Google Scholar 

Download references

Funding

No funding support our study.

Author information

Authors and Affiliations

  1. Department of Pediatric Surgery, Capital Institute of Pediatrics, Beijing, 100020, People’s Republic of China

    Hui Xiao, Rui Huang, Long Chen, Mei Diao & Long Li

  2. Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, People’s Republic of China

    Hui Xiao & Long Chen

Authors
  1. Hui Xiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rui Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Long Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mei Diao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Long Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Long Li.

Ethics declarations

Conflict of interest

All authors have contributed significantly and are in agreement with the content of the manuscript. All authors have no relevant financial relationships to disclose.

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Xiao, H., Huang, R., Chen, L. et al. Integrating lncRNAs and mRNAs expression profiles in terminal hindgut of fetal rats with anorectal malformations. Pediatr Surg Int 34, 971–982 (2018). https://doi.org/10.1007/s00383-018-4311-8

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00383-018-4311-8

Keywords

Search

Navigation