Abstract

Research Article

Gene Expression and Functional Analysis in Patients with Acute and Chronic Renal Allograft Rejection

Carlos Carmona*, Marlon Castrillón, John Fredy Nieto, Gustavo Zuluaga, Luis Fernando Arias and Cristian Álvarez

Published: 03 November, 2023 | Volume 7 - Issue 1 | Pages: 051-063

Kidney transplantation is the therapy of choice for patients with end-stage kidney disease (ESKD). Nevertheless, the main limitation for long-term graft survival is immune-mediated rejection. Some authors have proposed that differences in immune effector mechanisms are influenced by underlying molecular mechanisms; thereby, the identification of differentially expressed genes in acute or chronic rejection in non-invasive samples such as urine may be essential for the identification of potential biomarkers and biological processes associated with allograft outcomes. Our aim was to explore differences in gene expression and functional categories associated with acute and chronic kidney rejection in blood, biopsy, and urine of kidney transplant patients using RNA-Seq. RNA was isolated and sequenced implementing standard protocols. Analyses were addressed to identify differentially expressed genes (DEGs) and Functional Categories of Gene Ontology comparing between samples. Then we focused on immune genes and pathways to identify their association with the allograft. We identified a significant transcriptional similarity between biopsy and urine, in comparison with blood in acute and chronic rejection. Functional analyses suggested an enrichment of immune processes such as antigen processing and presentation, and regulation of B cell receptor signaling pathway in blood of acute and chronic rejection, respectively. Additionally, we observed an increase in expression of chemokines in biopsy and urine of both outcomes along with an increase in chemokine receptors in blood. Our findings suggest that urine is suitable for identifying potential biomarkers and biological processes related to renal allograft rejection, as it shares a significant number of regulated genes with biopsy.

Read Full Article HTML DOI: 10.29328/journal.abse.1001025 Cite this Article Read Full Article PDF

Keywords:

Kidney allograft; Allograft rejection; RNA-Seq; Gene expression; Biomarkers

References

  1. Lentine KL, Smith JM, Hart A, Miller J, Skeans MA, Larkin L, Robinson A, Gauntt K, Israni AK, Hirose R, Snyder JJ. OPTN/SRTR 2020 Annual Data Report: Kidney. Am J Transplant. 2022 Mar;22 Suppl 2:21-136. doi: 10.1111/ajt.16982. PMID: 35266618.
  2. Joosten SA, Sijpkens YW, van Kooten C, Paul LC. Chronic renal allograft rejection: pathophysiologic considerations. Kidney Int. 2005 Jul;68(1):1-13. doi: 10.1111/j.1523-1755.2005.00376.x. PMID: 15954891.
  3. Iwahara N, Hotta K, Iwami D, Tanabe T, Tanaka Y, Ito YM, Otsuka T, Murai S, Takada Y, Higuchi H, Sasaki H, Hirose T, Harada H, Shinohara N. Analysis of T-cell alloantigen response viaa direct pathway in kidney transplant recipients with donor-specific antibodies. Front Immunol. 2023 May 3;14:1164794. doi: 10.3389/fimmu.2023.1164794. PMID: 37207202; PMCID: PMC10189043.
  4. Etxebarria A, Díez-Martín E, Astigarraga E, Barreda-Gómez G. Role of the Immune System in Renal Transplantation, Types of Response, Technical Approaches and Current Challenges. 2022; 2(4): 548–570. https://doi.org/10.3390/immuno2040035
  5. Farrar CA, Kupiec-Weglinski JW, Sacks SH. The innate immune system and transplantation. Cold Spring Harb Perspect Med. 2013 Oct 1;3(10):a015479. doi: 10.1101/cshperspect.a015479. PMID: 24086066; PMCID: PMC3784815.
  6. Callemeyn J, Lamarthée B, Koenig A, Koshy P, Thaunat O, Naesens M. Allorecognition and the spectrum of kidney transplant rejection. Kidney Int. 2022 Apr;101(4):692-710. doi: 10.1016/j.kint.2021.11.029. Epub 2021 Dec 13. PMID: 34915041.
  7. Siu JHY, Surendrakumar V, Richards JA, Pettigrew GJ. T cell Allorecognition Pathways in Solid Organ Transplantation. Front Immunol. 2018 Nov 5;9:2548. doi: 10.3389/fimmu.2018.02548. PMID: 30455697; PMCID: PMC6230624.
  8. Grafals M, Thurman JM. The Role of Complement in Organ Transplantation. Front Immunol. 2019 Oct 4;10:2380. doi: 10.3389/fimmu.2019.02380. PMID: 31636644; PMCID: PMC6788431.
  9. Krupickova L, Fialova M, Novotny M, Svachova V, Mezerova K, Cecrdlova E, Viklicky O, Striz I. Chemokine Profiles Are Affected in Serum of Patients with Acute Rejection of Kidney Allograft. Mediators Inflamm. 2021 Mar 11;2021:5513690. doi: 10.1155/2021/5513690. PMID: 33776571; PMCID: PMC7979290.
  10. Wang S, Zhang C, Wang J, Yang C, Xu M, Rong R, Zhu T, Zhu D. Endothelial Cells in Antibody-Mediated Rejection of Kidney Transplantation: Pathogenesis Mechanisms and Therapeutic Implications. J Immunol Res. 2017;2017:8746303. doi: 10.1155/2017/8746303. Epub 2017 Feb 1. Erratum in: J Immunol Res. 2019 Mar 10;2019:9691679. PMID: 28255564; PMCID: PMC5309424.
  11. Chia PY, Teo A, Yeo TW. Overview of the Assessment of Endothelial Function in Humans. Front Med (Lausanne). 2020 Oct 7;7:542567. doi: 10.3389/fmed.2020.542567. PMID: 33117828; PMCID: PMC7575777.
  12. Kummer L, Zaradzki M, Vijayan V, Arif R, Weigand MA, Immenschuh S, Wagner AH, Larmann J. Vascular Signaling in Allogenic Solid Organ Transplantation - The Role of Endothelial Cells. Front Physiol. 2020 May 8;11:443. doi: 10.3389/fphys.2020.00443. PMID: 32457653; PMCID: PMC7227440.
  13. Venner JM, Famulski KS, Badr D, Hidalgo LG, Chang J, Halloran PF. Molecular landscape of T cell-mediated rejection in human kidney transplants: prominence of CTLA4 and PD ligands. Am J Transplant. 2014 Nov;14(11):2565-76. doi: 10.1111/ajt.12946. Epub 2014 Sep 12. PMID: 25219326.
  14. Wang Y, Zhang D, Hu X. A Three-Gene Peripheral Blood Potential Diagnosis Signature for Acute Rejection in Renal Transplantation. Front Mol Biosci. 2021 May 4;8:661661. doi: 10.3389/fmolb.2021.661661. PMID: 34017855; PMCID: PMC8129004.
  15. Jeong HJ. Diagnosis of renal transplant rejection: Banff classification and beyond. Kidney Res Clin Pract. 2020 Mar 31;39(1):17-31. doi: 10.23876/j.krcp.20.003. PMID: 32164120; PMCID: PMC7105630.
  16. Trajceska L, Severova-Andreevska G, Dzekova-Vidimliski P, Nikolov I, Selim G, Spasovski G, Rambabova-Busletik I, Ristovska V, Grcevska L, Sikole A. Complications and Risks of Percutaneous Renal Biopsy. Open Access Maced J Med Sci. 2019 Mar 29;7(6):992-995. doi: 10.3889/oamjms.2019.226. PMID: 30976347; PMCID: PMC6454172.
  17. Brachemi S, Bollée G. Renal biopsy practice: What is the gold standard? World J Nephrol. 2014 Nov 6;3(4):287-94. doi: 10.5527/wjn.v3.i4.287. PMID: 25374824; PMCID: PMC4220363.
  18. Sakai K, Oguchi H, Muramatsu M, Shishido S. Protocol graft biopsy in kidney transplantation. Nephrology (Carlton). 2018 Jul;23 Suppl 2:38-44. doi: 10.1111/nep.13282. PMID: 29968403.
  19. Martínez-Fernández M, Paramio JM, Dueñas M. RNA Detection in Urine: From RNA Extraction to Good Normalizer Molecules. J Mol Diagn. 2016 Jan;18(1):15-22. doi: 10.1016/j.jmoldx.2015.07.008. Epub 2015 Nov 14. PMID: 26586227.
  20. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PMID: 23104886; PMCID: PMC3530905.
  21. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010 Jan 1;26(1):139-40. doi: 10.1093/bioinformatics/btp616. Epub 2009 Nov 11. PMID: 19910308; PMCID: PMC2796818.
  22. Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A. BioMart--biological queries made easy. BMC Genomics. 2009 Jan 14;10:22. doi: 10.1186/1471-2164-10-22. PMID: 19144180; PMCID: PMC2649164.
  23. Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012 May;16(5):284-7. doi: 10.1089/omi.2011.0118. Epub 2012 Mar 28. PMID: 22455463; PMCID: PMC3339379.
  24. Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol. 2017 Nov 15;18(1):220. doi: 10.1186/s13059-017-1349-1. PMID: 29141660; PMCID: PMC5688663.
  25. Sawinski D, Poggio ED. Introduction to Kidney Transplantation: Long-Term Management Challenges. Clin J Am Soc Nephrol. 2021 Aug;16(8):1262-1263. doi: 10.2215/CJN.13440820. Epub 2021 Mar 10. PMID: 33692119; PMCID: PMC8455035.
  26. Guzzi F, Cirillo L, Buti E, Becherucci F, Errichiello C, Roperto RM, Hunter JP, Romagnani P. Urinary Biomarkers for Diagnosis and Prediction of Acute Kidney Allograft Rejection: A Systematic Review. Int J Mol Sci. 2020 Sep 19;21(18):6889. doi: 10.3390/ijms21186889. PMID: 32961825; PMCID: PMC7555436.
  27. Snopkowski C, Salinas T, Li C, Stryjniak G, Ding R, Sharma V, Suthanthiran M. Urinary cell mRNA profiling of kidney allograft recipients: A systematic investigation of a filtration based protocol for the simplification of urine processing. J Immunol Methods. 2021 Nov;498:113132. doi: 10.1016/j.jim.2021.113132. Epub 2021 Aug 28. PMID: 34464607; PMCID: PMC8487946.
  28. Seo JW, Lee YH, Tae DH, Park SH, Moon JY, Jeong KH, Kim CD, Chung BH, Park JB, Kim YH, Seok J, Joo SH, Lee SH, Lee JS, Lee SH. Non-Invasive Diagnosis for Acute Rejection Using Urinary mRNA Signature Reflecting Allograft Status in Kidney Transplantation. Front Immunol. 2021 Jun 10;12:656632. doi: 10.3389/fimmu.2021.656632. Erratum in: Front Immunol. 2022 Jan 06;12:825243. PMID: 34177898; PMCID: PMC8222723.
  29. Rychkov D, Sur S, Sirota M, Sarwal MM. Molecular Diversity of Clinically Stable Human Kidney Allografts. JAMA Netw Open. 2021 Jan 4;4(1):e2035048. doi: 10.1001/jamanetworkopen.2020.35048. PMID: 33492376; PMCID: PMC7835722.
  30. Frangogiannis NG. The In fl ammatory Response in Tissue Repair 60 . 2 Initiation of the In fl ammatory Response Following Injury : The Alarmins. 2018; 1517–1537.
  31. Mata R, Yao Y, Cao W, Ding J, Zhou T, Zhai Z, Gao C. The Dynamic Inflammatory Tissue Microenvironment: Signality and Disease Therapy by Biomaterials. Research (Wash D C). 2021 Feb 3;2021:4189516. doi: 10.34133/2021/4189516. PMID: 33623917; PMCID: PMC7879376.
  32. Soliman AM, Barreda DR. Acute Inflammation in Tissue Healing. Int J Mol Sci. 2022 Dec 30;24(1):641. doi: 10.3390/ijms24010641. PMID: 36614083; PMCID: PMC9820461.
  33. Torres IB, Moreso F, Sarró E, Meseguer A, Serón D. The Interplay between inflammation and fibrosis in kidney transplantation. Biomed Res Int. 2014;2014:750602. doi: 10.1155/2014/750602. Epub 2014 Jun 4. PMID: 24991565; PMCID: PMC4065724.
  34. Schrijvers BF, Flyvbjerg A, De Vriese AS. The role of vascular endothelial growth factor (VEGF) in renal pathophysiology. Kidney Int. 2004 Jun;65(6):2003-17. doi: 10.1111/j.1523-1755.2004.00621.x. PMID: 15149314.
  35. Gielis EM, Anholts JDH, van Beelen E, Haasnoot GW, De Fijter HW, Bajema I, Heidt S, van de Vrie M, Hilbrands LB, Mallat MJK, Ledeganck KJ, Claas FHJ, Eikmans M. A Combined microRNA and Chemokine Profile in Urine to Identify Rejection After Kidney Transplantation. Transplant Direct. 2021 Jun 10;7(7):e711. doi: 10.1097/TXD.0000000000001169. PMID: 34131583; PMCID: PMC8196093.
  36. Mühlbacher J, Doberer K, Kozakowski N, Regele H, Camovic S, Haindl S, Bond G, Haslacher H, Eskandary F, Reeve J, Böhmig GA, Wahrmann M. Non-invasive Chemokine Detection: Improved Prediction of Antibody-Mediated Rejection in Donor-Specific Antibody-Positive Renal Allograft Recipients. Front Med (Lausanne). 2020 Apr 9;7:114. doi: 10.3389/fmed.2020.00114. PMID: 32328494; PMCID: PMC7160229.
  37. Handschin J, Wehmeier C, Amico P, Hopfer H, Dickenmann M, Schaub S, Hirt-Minkowski P. Urinary CXCL10 Measurement in Late Renal Allograft Biopsies Predicts Outcome Even in Histologically Quiescent Patients. Transplant Proc. 2021 Sep;53(7):2168-2179. doi: 10.1016/j.transproceed.2021.07.013. Epub 2021 Aug 19. PMID: 34419254.
  38. Hughes CE, Nibbs RJB. A guide to chemokines and their receptors. FEBS J. 2018 Aug;285(16):2944-2971. doi: 10.1111/febs.14466. Epub 2018 Apr 24. PMID: 29637711; PMCID: PMC6120486.
  39. Lim JH, Chung BH, Lee SH, Jung HY, Choi JY, Cho JH, Park SH, Kim YL, Kim CD. Omics-based biomarkers for diagnosis and prediction of kidney allograft rejection. Korean J Intern Med. 2022 May;37(3):520-533. doi: 10.3904/kjim.2021.518. Epub 2022 Apr 15. PMID: 35417937; PMCID: PMC9082440.
  40. Oweira H, Ramouz A, Ghamarnejad O, Khajeh E, Ali-Hasan-Al-Saegh S, Nikbakhsh R, Reißfelder C, Rahbari N, Mehrabi A, Sadeghi M. Risk Factors of Rejection in Renal Transplant Recipients: A Narrative Review. J Clin Med. 2022 Mar 3;11(5):1392. doi: 10.3390/jcm11051392. PMID: 35268482; PMCID: PMC8911293.

Figures:

Figure 1

Figure 1

Figure 1

Figure 2

Figure 1

Figure 3

Figure 1

Figure 4

Figure 1

Figure 5

Figure 1

Figure 6

Figure 1

Figure 7

Similar Articles

Recently Viewed

Read More

Most Viewed

Read More

Help ?