Display options
Cite
Ma Y, Dammer EB, Felsky D, et al. Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue. Nat Commun. 2021;12(1):7035doi: 10.1038/s41467-021-27204-9.
Ma, Y., Dammer, E. B., Felsky, D., Duong, D. M., Klein, H. U., White, C. C., Zhou, M., Logsdon, B. A., McCabe, C., Xu, J., Wang, M., Wingo, T. S., Lah, J. J., Zhang, B., Schneider, J., Allen, M., Wang, X., Ertekin-Taner, N., Seyfried, N. T., Levey, A. I., Bennett, D. A., & De Jager, P. L. (2021). Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue. Nature communications, 12(1), 7035. https://doi.org/10.1038/s41467-021-27204-9
Ma, Yiyi, et al. "Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue." Nature communications vol. 12,1 (2021): 7035. doi: https://doi.org/10.1038/s41467-021-27204-9
Ma Y, Dammer EB, Felsky D, Duong DM, Klein HU, White CC, Zhou M, Logsdon BA, McCabe C, Xu J, Wang M, Wingo TS, Lah JJ, Zhang B, Schneider J, Allen M, Wang X, Ertekin-Taner N, Seyfried NT, Levey AI, Bennett DA, De Jager PL. Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue. Nat Commun. 2021 Dec 02;12(1):7035. doi: 10.1038/s41467-021-27204-9. PMID: 34857756; PMCID: PMC8640037.
Copy Download .nbib Format: NLM
Share it on

Nat Commun. 2021 Dec 02;12(1):7035. doi: 10.1038/s41467-021-27204-9.

Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue.

Nature communications

Yiyi Ma, Eric B Dammer, Daniel Felsky, Duc M Duong, Hans-Ulrich Klein, Charles C White, Maotian Zhou, Benjamin A Logsdon, Cristin McCabe, Jishu Xu, Minghui Wang, Thomas S Wingo, James J Lah, Bin Zhang, Julie Schneider, Mariet Allen, Xue Wang, Nilüfer Ertekin-Taner, Nicholas T Seyfried, Allan I Levey, David A Bennett, Philip L De Jager

Affiliations

  1. Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th street, New York, NY, 10032, USA.
  2. Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
  3. Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA, 30322, USA.
  4. Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
  5. Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
  6. Cell Circuits Program, Broad Institute, 415 Main street, Cambridge, MA, 02142, USA.
  7. Sage Bionetworks, 2901 Third Avenue, Suite 330, Seattle, WA, 98121, USA.
  8. Rush Alzheimer's Disease Center, Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, 60612, USA.
  9. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
  10. Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
  11. Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
  12. Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA.
  13. Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
  14. Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL, 32224, USA.
  15. Mayo Clinic Florida, Department of Health Sciences Research, Jacksonville, FL, 32224, USA.
  16. Mayo Clinic Florida, Department of Neurology, Jacksonville, FL, 32224, USA.
  17. Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th street, New York, NY, 10032, USA. [email protected].
  18. Cell Circuits Program, Broad Institute, 415 Main street, Cambridge, MA, 02142, USA. [email protected].

PMID: 34857756 PMCID: PMC8640037 DOI: 10.1038/s41467-021-27204-9

Abstract

RNA editing is a feature of RNA maturation resulting in the formation of transcripts whose sequence differs from the genome template. Brain RNA editing may be altered in Alzheimer's disease (AD). Here, we analyzed data from 1,865 brain samples covering 9 brain regions from 1,074 unrelated subjects on a transcriptome-wide scale to identify inter-regional differences in RNA editing. We expand the list of known brain editing events by identifying 58,761 previously unreported events. We note that only a small proportion of these editing events are found at the protein level in our proteome-wide validation effort. We also identified the occurrence of editing events associated with AD dementia, neuropathological measures and longitudinal cognitive decline in: SYT11, MCUR1, SOD2, ORAI2, HSDL2, PFKP, and GPRC5B. Thus, we present an extended reference set of brain RNA editing events, identify a subset that are found to be expressed at the protein level, and extend the narrative of transcriptomic perturbation in AD to RNA editing.

© 2021. The Author(s).

References

  1. Nat Med. 2016 Oct;22(10):1140-1150 - PubMed
  2. Nature. 2003 Aug 14;424(6950):778-83 - PubMed
  3. RNA. 2013 Jun;19(6):725-32 - PubMed
  4. Nat Genet. 2017 Sep;49(9):1373-1384 - PubMed
  5. Sci Data. 2018 Sep 11;5:180185 - PubMed
  6. Nature. 2017 Oct 11;550(7675):249-254 - PubMed
  7. Bioinformatics. 2013 Jan 1;29(1):15-21 - PubMed
  8. Nat Protoc. 2018 Jul;13(7):1632-1661 - PubMed
  9. Sci Data. 2018 Aug 07;5:180142 - PubMed
  10. Acta Neuropathol. 2018 Nov;136(5):709-727 - PubMed
  11. Cell Death Dis. 2018 Sep 24;9(10):988 - PubMed
  12. Nucleic Acids Res. 2014 Jan;42(Database issue):D109-13 - PubMed
  13. Alzheimers Dement. 2021 Jun;17(6):984-1004 - PubMed
  14. PLoS One. 2010 Apr 26;5(4):e10351 - PubMed
  15. PLoS One. 2012;7(1):e28033 - PubMed
  16. Neuron. 2018 Jul 11;99(1):64-82.e7 - PubMed
  17. Sci Rep. 2018 Mar 9;8(1):4282 - PubMed
  18. Genomics. 2000 Apr 15;65(2):121-8 - PubMed
  19. Biochem Biophys Res Commun. 2017 Feb 19;483(4):998-1004 - PubMed
  20. Lancet. 2002 Sep 14;360(9336):842-9 - PubMed
  21. J Alzheimers Dis. 2016 Mar 16;52(2):483-95 - PubMed
  22. Nat Commun. 2017 Mar 15;8:14714 - PubMed
  23. Neurosci Res. 2018 Nov;136:33-47 - PubMed
  24. Nat Genet. 2018 Nov;50(11):1584-1592 - PubMed
  25. Alzheimers Dement. 2018 Mar;14(3):352-366 - PubMed
  26. Antioxid Redox Signal. 2018 Sep 20;29(9):846-863 - PubMed
  27. Science. 2011 Jul 1;333(6038):53-8 - PubMed
  28. J Proteome Res. 2006 Feb;5(2):277-86 - PubMed
  29. BMC Bioinformatics. 2011 Aug 04;12:323 - PubMed
  30. PLoS One. 2013;8(2):e57395 - PubMed
  31. Sci Rep. 2015 Oct 09;5:14941 - PubMed
  32. Cell Calcium. 2018 Mar;70:87-94 - PubMed
  33. Nat Neurosci. 2019 Jan;22(1):37-46 - PubMed
  34. Nat Methods. 2012 Jun;9(6):579-81 - PubMed
  35. Neurobiol Aging. 2014 Aug;35(8):1785-91 - PubMed
  36. J Proteome Res. 2017 Sep 1;16(9):3336-3347 - PubMed
  37. Cell. 1987 Sep 11;50(6):831-40 - PubMed
  38. Sci Data. 2016 Oct 11;3:160089 - PubMed
  39. Mol Neurodegener. 2017 Nov 6;12(1):82 - PubMed
  40. Epilepsia. 2017 Apr;58(4):e59-e63 - PubMed
  41. Cell Rep. 2017 Oct 10;21(2):366-380 - PubMed
  42. Nat Cell Biol. 2015 Jul;17(7):953 - PubMed
  43. Genomics. 2000 Jul 1;67(1):8-18 - PubMed
  44. J Biol Chem. 2011 Dec 30;286(52):44557-68 - PubMed

Publication Types

Grant support