SpringerLink
Log in

Distinct global DNA methylation and NF-κB expression profile of preimplantation biopsies from ideal and non-ideal kidneys

  • Original Article
  • Published:
Journal of Nephrology Aims and scope Submit manuscript

Abstract

Background

Epigenetic mechanisms may affect the ideal and non-ideal kidneys selected for transplantation and their inflammatory gene expression profile differently and may contribute to poor clinical outcomes.

Objective

Study the Global DNA methylation and the expression profiles of the DNA methyltransferases (DNMTs) and nuclear factor kappa B (NF-κB) in preimplantation kidney biopsies from ideal and non-ideal kidneys (expanded criteria donor (ECD) and with KDPI > 85%).

Methods

In a sample consisting of 45 consecutive pre-implantation biopsies, global DNA methylation levels were detected by LINE-1 repeated elements using bisulfite pyrosequencing. DNMT gene expression was assessed by real-time quantitative polymerase chain reaction, and NF-κB protein expression by immunofluorescence.

Results

ECD kidneys displayed increased methylation levels in LINE-1, and DNMT1 and DNMT3B expression was upregulated when comparing ECD to standard criteria donor kidneys. Similarly, kidneys with KDPI > 85% exhibited increased LINE-1 methylation and DNMT1 upregulation when compared to a KDPI ≤ 85%. NF-κB protein expression levels were greatly increased in both types of non-ideal kidneys compared to ideal kidneys. Moreover, hypermethylation of LINE-1 was associated with cold ischemia time > 20 h and ECD kidney classification.

Conclusions

This study shows that global DNA hypermethylation and high expression of NF-κB occurred in both types of non-ideal kidneys and were associated with prolonged cold ischemia time. Global DNA methylation can be a useful tool to assess non-ideal kidneys and hence, could be used to expand the pool of kidneys donors.

Graphical abstract

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (Germany)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Data availability statement

The data that support the findings of this study are available from the corresponding author upon reasonable request.

References

  1. Mittal S, Adamusiak A, Horsfield C et al (2017) A re-evaluation of discarded deceased donor kidneys in the UK: are usable organs still being discarded? Transplantation 101(7):1698–1703

    Article  Google Scholar 

  2. Wong G, Howell M, Patrick E, Yang J (2017) Taking kidneys for granted? Time to reflect on the choices we make. Transplantation 101(12):2812–2813

    Article  Google Scholar 

  3. McKay DB (2011) The role of innate immunity in donor organ procurement. Semin Immunopathol 33(2):169–184

    Article  Google Scholar 

  4. Zhao H, Alam A, Soo AP, George AJT, Ma D (2018) Ischemia-reperfusion injury reduces long term renal graft survival: mechanism and beyond. EBioMedicine 28:31–42

    Article  Google Scholar 

  5. Mazeti-Felicio CM, Caldas HC, Fernandes-Charpiot IMM, Dezotti CZ, Baptista MASF, Abbud-Filho M (2017) Preimplantation kidney biopsies of extended criteria donors have a heavier inflammatory burden than kidneys from standard criteria donors. Transplant Direct 3(7):e180

    Article  CAS  Google Scholar 

  6. Heylen L, Thienpont B, Naesens M et al (2018) Ischemia-induced DNA hypermethylation during kidney transplant predicts chronic allograft injury. J Am Soc Nephrol 29(5):1566–1576

    Article  CAS  Google Scholar 

  7. Rousselle T, Bardhi E, Maluf DG, Mas VR (2021) Epigenetic modifications and the development of kidney graft fibrosis [published correction appears in Curr Opin Organ Transplant. 26(3), 346 (2021)]. Curr Opin Organ Transplant. 26(1):1–9

    Article  CAS  Google Scholar 

  8. Agodi A, Barchitta M, Maugeri A, et al. Unveiling the role of DNA methylation in kidney transplantation: novel perspectives toward biomarker identification. Biomed Res Int. 2019:1602539.

  9. Gujar H, Weisenberger DJ, Liang G (2019) The roles of human DNA methyltransferases and their isoforms in sha** the epigenome. Genes (Basel) 10(2):172

    Article  CAS  Google Scholar 

  10. Ohka F, Natsume A, Motomura K et al (2011) The global DNA methylation surrogate LINE-1 methylation is correlated with MGMT promoter methylation and is a better prognostic factor for glioma. PLoS ONE 6(8):e23332

    Article  CAS  Google Scholar 

  11. Roman-Gomez J, Jimenez-Velasco A, Agirre X et al (2005) Promoter hypomethylation of the LINE-1 retrotransposable elements activates sense/antisense transcription and marks the progression of chronic myeloid leukemia. Oncogene 24(48):7213–7223

    Article  CAS  Google Scholar 

  12. Kitkumthorn N, Mutirangura A (2011) Long interspersed nuclear element-1 hypomethylation in cancer: biology and clinical applications. Clin Epigenet 2(2):315–330

    Article  CAS  Google Scholar 

  13. Molinero LL, Alegre ML (2012) Role of T cell-nuclear factor κB in transplantation. Transplant Rev 26(3):189–200

    Article  Google Scholar 

  14. Florim GMS, Caldas HC, Gonçalves NN et al (2020) Activation of HMGB1-TLR4 pathway and inflammasome contribute to enhanced inflammatory response in extended criteria and kidneys with KDPI ≥85. Transplantation 104(4):724–730

    Article  CAS  Google Scholar 

  15. Metzger RA, Delmonico FL, Feng S, Port FK, Wynn JJ, Merion RM (2003) Expanded criteria donors for kidney transplantation. Am J Transplant 3(4):114–125

    Article  Google Scholar 

  16. Rao PS, Schaubel DE, Guidinger MK et al (2009) A comprehensive risk quantification score for deceased donor kidneys: the kidney donor risk index. Transplantation 88(2):231–236

    Article  Google Scholar 

  17. Wong JY, De Vivo I, Lin X, Grashow R, Cavallari J, Christiani DC (2014) The association between global DNA methylation and telomere length in a longitudinal study of boilermakers. Genet Epidemiol 38(3):254–264

    Article  Google Scholar 

  18. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25:402–408

    Article  CAS  Google Scholar 

  19. Moore LD, Le T, Fan G (2013) DNA methylation and its basic function. Neuropsychopharmacology 38(1):23–38

    Article  CAS  Google Scholar 

  20. Dressler GR, Patel SR (2015) Epigenetics in kidney development and renal disease. Transl Res 165(1):166–176

    Article  CAS  Google Scholar 

  21. Bestor TH (2000) The DNA methyltransferases of mammals. Hum Mol Genet 9(16):2395–2402

    Article  CAS  Google Scholar 

  22. Edwards JR, Yarychkivska O, Boulard M, Bestor TH (2017) DNA methylation and DNA methyltransferases. Epigenet Chromatin 10:23

    Article  Google Scholar 

  23. Puto LA, Reed JC (2008) Daxx represses RelB target promoters via DNA methyltransferase recruitment and DNA hypermethylation. Genes Dev 22(8):998–1010

    Article  CAS  Google Scholar 

  24. Gorayeb-Polacchini FS, Caldas HC, Fernandes-Charpiot IMM, Ferreira-Baptista MAS, Gauch CR, Abbud-Filho M (2020) Impact of cold ischemia time on kidney transplant: a mate kidney analysis. Transplant Proc 52(5):1269–1271

    Article  Google Scholar 

  25. de Sandes-Freitas TV, Mazzali M, Manfro RC et al (2021) Exploring the causes of the high incidence of delayed graft function after kidney transplantation in Brazil: a multicenter study. Transpl Int 34(6):1093–1104

    Article  Google Scholar 

  26. Bestard O, Cuñetti L, Cruzado JM et al (2011) Intragraft regulatory T cells in protocol biopsies retain foxp3 demethylation and are protective biomarkers for kidney graft outcome. Am J Transplant 11:544–550

    Article  Google Scholar 

  27. Bechtel W, McGoohan S, Zeisberg EM et al (2010) Methylation determines fibroblast activation and fibrogenesis in the kidney. Nat Med 16(5):544–550

    Article  CAS  Google Scholar 

  28. Parker MD, Chambers PA, Lodge JP, Pratt JR (2008) Ischemia-reperfusion injury and its influence on the epigenetic modification of the donor kidney genome. Transplantation 86(12):1818–1823

    Article  Google Scholar 

  29. Pavanello S, Campisi M, Fabozzo A et al (2020) The biological age of the heart is consistently younger than chronological age. Sci Rep 10(1):10752

    Article  CAS  Google Scholar 

  30. Heylen L, Thienpont B, Busschaert P et al (2019) Age-related changes in DNA methylation affect renal histology and post-transplant fibrosis. Kidney Int 96(5):1195–1204

    Article  CAS  Google Scholar 

  31. Zhu C, **ang W, Li B et al (2021) DNA methylation modulates allograft survival and acute rejection after renal transplantation by regulating the mTOR pathway. Am J Transplant 21(2):567–581

    Article  CAS  Google Scholar 

  32. Rousselle T, Bardhi E, Maluf DG, Mas VR (2021) Epigenetic modifications and the development of kidney graft fibrosis. Curr Opin Organ Transplant 26(1):1–9

    Article  CAS  Google Scholar 

  33. Lu T, Stark GR (2015) NF-κB: Regulation by Methylation. Cancer Res 75(18):3692–3695

    Article  CAS  Google Scholar 

  34. Sun SC, Chang JH, ** J (2013) Regulation of nuclear factor-κB in autoimmunity. Trends Immunol 34(6):282–289

    Article  CAS  Google Scholar 

  35. Mas VR, Le TH, Maluf DG (2016) Epigenetics in kidney transplantation: current evidence, predictions, and future research directions. Transplantation 100(1):23–38

    Article  CAS  Google Scholar 

  36. Hashmp SF, Sattar MZA, Rathore HA, Ahmadi A, Johns EJ (2017) A critical review on pharmacological significance of hydrogen sulfide (H2S) on NF-ΚB concentration and icam-1 expression in renal ischemia reperfusion injury. Acta Pol Pharm 74(3):747–752

    PubMed  Google Scholar 

  37. Rajabi H, Tagde A, Alam M et al (2016) DNA methylation by DNMT1 and DNMT3b methyltransferases is driven by the MUC1-C oncoprotein in human carcinoma cells. Oncogene 35(50):6439–6445

    Article  CAS  Google Scholar 

  38. Liu Y, Mayo MW, Nagji AS et al (2012) Phosphorylation of RelA/p65 promotes DNMT-1 recruitment to chromatin and represses transcription of the tumor metastasis suppressor gene BRMS1. Oncogene 31(9):1143–1154

    Article  Google Scholar 

Download references

Acknowledgements

This study was supported by São Paulo State Research Foundation (FAPESP–Fundação de Amparo à Pesquisa do Estado de São Paulo) Grant Number 2016/08301-8.

Author information

Author notes

  1. Naiane do Nascimento Gonçalves and Heloisa Cristina Caldas have contributed equally to this manuscript.

Authors and Affiliations

  1. Department of Medicine, Faculdade de Medicina de São José do Rio Preto (FAMERP), Laboratório de Imunologia e Transplante Experimental (LITEX), Hospital de Base, Av. Brigadeiro Faria Lima, 5416, São Jose do Rio Preto, SP, 15090-000, Brazil

    Naiane do Nascimento Gonçalves, Heloisa Cristina Caldas, Greiciane Maria da Silva Florim, Giovanna Mattiello Sormani, Maria Alice Sperto Ferreira Baptista, Ida Maria Maximina Fernandes-Charpiot & Mario Abbud-Filho

  2. Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil

    Lidia Maria Rebolho Batista Arantes & Bruna Pereira Sorroche

  3. Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA

    Carlos Henrique Viese Nascimento-Filho & Rogério Moraes de Castilho

Authors
  1. Naiane do Nascimento Gonçalves
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Heloisa Cristina Caldas
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Greiciane Maria da Silva Florim
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Giovanna Mattiello Sormani
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lidia Maria Rebolho Batista Arantes
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Bruna Pereira Sorroche
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Maria Alice Sperto Ferreira Baptista
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ida Maria Maximina Fernandes-Charpiot
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Carlos Henrique Viese Nascimento-Filho
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Rogério Moraes de Castilho
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Mario Abbud-Filho
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mario Abbud-Filho.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethics approval

This study was approved by the institution’s Medical School Research Ethics Committee (# 2.003.464), following current standards for research involving human beings.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 115 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

do Nascimento Gonçalves, N., Caldas, H.C., da Silva Florim, G.M. et al. Distinct global DNA methylation and NF-κB expression profile of preimplantation biopsies from ideal and non-ideal kidneys. J Nephrol 35, 1831–1840 (2022). https://doi.org/10.1007/s40620-022-01341-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s40620-022-01341-w

Keywords

Search

Navigation