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FISHing for Chromosome Instability and Aneuploidy in the Alzheimer’s Disease Brain

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Alzheimer’s Disease

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2561))

Abstract

Fluorescence in situ hybridization (FISH) is the method of choice for visualizing chromosomal DNA in post-mitotic cells. The availability of chromosome-enumeration (centromeric), site-specific, and multicolor-banding DNA probes offers opportunities to uncover genomic changes, at the chromosomal level, in single interphase nuclei. Alzheimer’s disease (AD) has been associated repeatedly with (sub)chromosome instability and aneuploidy, likely affecting the brain. Although the types and rates of chromosome instability in the AD brain remain a matter of debate, molecular cytogenetic analysis of brain cells appears to be important for uncovering mechanisms of neurodegeneration. Here, we describe a FISH protocol for studying chromosome instability and aneuploidy in the AD brain.

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References

  1. Iourov IY, Vorsanova SG, Yurov YB (2006) Chromosomal variation in mammalian neuronal cells: known facts and attractive hypotheses. Int Rev Cytol 249:143–191. https://doi.org/10.1016/S0074-7696(06)49003-3

    Article  CAS  PubMed  Google Scholar 

  2. Kingsbury MA, Yung YC, Peterson SE et al (2006) Aneuploidy in the normal and diseased brain. Cell Mol Life Sci 63:2626–2641. https://doi.org/10.1007/s00018-006-6169-5

    Article  CAS  PubMed  Google Scholar 

  3. Vorsanova SG, Yurov YB, Iourov IY (2010) Human interphase chromosomes: a review of available molecular cytogenetic technologies. Mol Cytogenet 3:1. https://doi.org/10.1186/1755-8166-3-1. (an open-access article distributed under the terms of the Creative Commons Attribution License)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Bakker B, van den Bos H, Lansdorp PM et al (2015) How to count chromosomes in a cell: an overview of current and novel technologies. BioEssays 37(5):570–577. https://doi.org/10.1002/bies.201400218

    Article  PubMed  Google Scholar 

  5. Hu Q, Maurais EG, Ly P (2020) Cellular and genomic approaches for exploring structural chromosomal rearrangements. Chromosom Res 28(1):19–30. https://doi.org/10.1007/s10577-020-09626-1

    Article  CAS  Google Scholar 

  6. Westra JW, Barral S, Chun J (2009) A reevaluation of tetraploidy in the Alzheimer’s disease brain. Neurodegener Dis 6(5–6):221–229. https://doi.org/10.1159/000236901

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Vorsanova SG, Yurov YB, Iourov IY (2013) Technological solutions in human interphase cytogenetics. In: Yurov Y, Vorsanova S, Iourov I (eds) Human interphase chromosomes. Springer, New York, pp 179–203. https://doi.org/10.1007/978-1-4614-6558-4_11

    Chapter  Google Scholar 

  8. Mosch B, Morawski M, Mittag A et al (2007) Aneuploidy and DNA replication in the normal human brain and Alzheimer’s disease. J Neurosci 27(26):6859–6867. https://doi.org/10.1523/JNEUROSCI.0379-07.2007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Arendt T, Mosch B, Morawski M (2009) Neuronal aneuploidy in health and disease: a cytomic approach to understand the molecular individuality of neurons. Int J Mol Sci 10(4):1609–1627. https://doi.org/10.3390/ijms10041609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Iourov IY, Vorsanova SG, Liehr T et al (2009) Aneuploidy in the normal, Alzheimer’s disease and ataxia-telangiectasia brain: differential expression and pathological meaning. Neurobiol Dis 34(2):212–220. https://doi.org/10.1016/j.nbd.2009.01.003

    Article  CAS  PubMed  Google Scholar 

  11. Bushman DM, Kaeser GE, Siddoway B et al (2015) Genomic mosaicism with increased amyloid precursor protein (APP) gene copy number in single neurons from sporadic Alzheimer’s disease brains. elife 4:e05116. https://doi.org/10.7554/eLife.05116

    Article  PubMed Central  Google Scholar 

  12. Iourov IY, Yurov YB, Vorsanova SG et al (2021) Chromosome instability, aging and brain diseases. Cell 10(5):1256. https://doi.org/10.3390/cells10051256

    Article  CAS  Google Scholar 

  13. Arendt T, Brückner MK, Mosch B et al (2010) Selective cell death of hyperploid neurons in Alzheimer’s disease. Am J Pathol 177(1):15–20. https://doi.org/10.2353/ajpath.2010.090955

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Yurov YB, Vorsanova SG, Iourov IY (2011) The DNA replication stress hypothesis of Alzheimer’s disease. ScientificWorldJournal 11:2602–2612. https://doi.org/10.1100/2011/625690

    Article  CAS  PubMed  Google Scholar 

  15. Bajic V, Spremo-Potparevic B, Zivkovic L et al (2015) Cohesion and the aneuploid phenotype in Alzheimer’s disease: a tale of genome instability. Neurosci Biobehav Rev 55:365–374. https://doi.org/10.1016/j.neubiorev.2015.05.010

    Article  CAS  PubMed  Google Scholar 

  16. Leija-Salazar M, Piette C, Proukakis C (2018) Review: somatic mutations in neurodegeneration. Neuropathol Appl Neurobiol 44(3):267–285. https://doi.org/10.1111/nan.12465

    Article  CAS  PubMed  Google Scholar 

  17. Bushman DM, Chun J (2013) The genomically mosaic brain: aneuploidy and more in neural diversity and disease. Semin Cell Dev Biol 24(4):357–369. https://doi.org/10.1016/j.semcdb.2013.02.003

    Article  PubMed  PubMed Central  Google Scholar 

  18. Rohrback S, Siddoway B, Liu CS et al (2018) Genomic mosaicism in the developing and adult brain. Dev Neurobiol 78(11):1026–1048. https://doi.org/10.1002/dneu.22626

    Article  PubMed  PubMed Central  Google Scholar 

  19. Yurov YB, Vorsanova SG, Iourov IY (2018) Human molecular neurocytogenetics. Curr Genet Med Rep 6:155–164. https://doi.org/10.1007/s40142-018-0152-y

    Article  Google Scholar 

  20. Iourov IY, Vorsanova SG, Yurov YB et al (2019) Ontogenetic and pathogenetic views on somatic chromosomal mosaicism. Genes 10(5):379

    Article  CAS  PubMed Central  Google Scholar 

  21. Yurov YB, Vorsanova SG, Iourov IY (2019) Chromosome instability in the neurodegenerating brain. Front Genet 10:892. https://doi.org/10.3389/fgene.2019.00892

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Jourdon A, Fasching L, Scuderi S et al (2020) The role of somatic mosaicism in brain disease. Curr Opin Genet Dev 65:84–90. https://doi.org/10.1016/j.gde.2020.05.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kaeser GE, Chun J (2020) Mosaic somatic gene recombination as a potentially unifying hypothesis for Alzheimer’s disease. Front Genet 11:390. https://doi.org/10.3389/fgene.2020.00390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Iourov IY, Vorsanova SG, Yurov YB (2012) Single cell genomics of the brain: focus on neuronal diversity and neuropsychiatric diseases. Curr Genomics 13(6):477–488. https://doi.org/10.2174/138920212802510439

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Iourov IY, Vorsanova SG, Yurov YB (2011) Genomic landscape of the Alzheimer’s disease brain: chromosome instability — aneuploidy, but not tetraploidy — mediates neurodegeneration. Neurodegener Dis 8(1–2):35–37.; discussion 38-40. https://doi.org/10.1159/000315398

    Article  PubMed  Google Scholar 

  26. Andriani GA, Maggi E, Piqué D et al (2019) A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknesses. Sci Rep 9(1):10508. https://doi.org/10.1038/s41598-019-46606-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Liehr T (2017) Fluorescence in situ hybridization (FISH). Springer, Berlin/Heidelberg

    Book  Google Scholar 

  28. Iourov IY, Liehr T, Vorsanova SG et al (2007) Interphase chromosome-specific multicolor banding (ICS-MCB): a new tool for analysis of interphase chromosomes in their integrity. Biomol Eng 24(4):415–417. https://doi.org/10.1016/j.bioeng.2007.05.003

    Article  CAS  PubMed  Google Scholar 

  29. Liehr T, Othman MA, Rittscher K (2017) Multicolor karyotyping and fluorescence in situ hybridization-banding (MCB/mBAND). Methods Mol Biol 1541:181–187. https://doi.org/10.1007/978-1-4939-6703-2_16

    Article  CAS  PubMed  Google Scholar 

  30. Iourov IY, Liehr T, Vorsanova SG et al (2006) Visualization of interphase chromosomes in postmitotic cells of the human brain by multicolour banding (MCB). Chromosom Res 14(3):223–229. https://doi.org/10.1007/s10577-006-1037-6

    Article  CAS  Google Scholar 

  31. Manvelyan M, Hunstig F, Mrasek K et al (2008) Position of chromosomes 18, 19, 21 and 22 in 3D-preserved interphase nuclei of human and gorilla and white hand gibbon. Mol Cytogenet 1:9. https://doi.org/10.1186/1755-8166-1-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Yurov YB, Iourov IY, Vorsanova SG et al (2008) The schizophrenia brain exhibits low-level aneuploidy involving chromosome 1. Schizophr Res 98(1–3):139–147. https://doi.org/10.1016/j.schres.2007.07.035

    Article  PubMed  Google Scholar 

  33. Iourov IY, Vorsanova SG, Kurinnaia OS et al (2021) Causes and consequences of genome instability in psychiatric and neurodegenerative diseases. Mol Biol 55(1):37–46. https://doi.org/10.1134/S0026893321010155

    Article  CAS  Google Scholar 

  34. Hou Y, Song H, Croteau DL et al (2017) Genome instability in Alzheimer disease. Mech Ageing Dev 161(Pt A):83–94. https://doi.org/10.1016/j.mad.2016.04.005

    Article  CAS  PubMed  Google Scholar 

  35. Nudelman KNH, McDonald BC, Lahiri DK et al (2019) Biological hallmarks of cancer in Alzheimer’s disease. Mol Neurobiol 56(10):7173–7187. https://doi.org/10.1007/s12035-019-1591-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Neuner SM, Tcw J, Goate AM (2020) Genetic architecture of Alzheimer’s disease. Neurobiol Dis 143:104976. https://doi.org/10.1016/j.nbd.2020.104976

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Vorsanova SG, Yurov YB, Iourov IY (2020) Dynamic nature of somatic chromosomal mosaicism, genetic-environmental interactions and therapeutic opportunities in disease and aging. Mol Cytogenet 13:16. https://doi.org/10.1186/s13039-020-00488-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. van Leeuwen LA, Hoozemans JJ (2015) Physiological and pathophysiological functions of cell cycle proteins in post-mitotic neurons: implications for Alzheimer’s disease. Acta Neuropathol 129(4):511–525. https://doi.org/10.1007/s00401-015-1382-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Caneus J, Granic A, Rademakers R et al (2018) Mitotic defects lead to neuronal aneuploidy and apoptosis in frontotemporal lobar degeneration caused by MAPT mutations. Mol Biol Cell 29(5):575–586. https://doi.org/10.1091/mbc.E17-01-0031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Potter H, Chial HJ, Caneus J et al (2019) Chromosome instability and mosaic aneuploidy in neurodegenerative and neurodevelopmental disorders. Front Genet 10:1092. https://doi.org/10.3389/fgene.2019.01092

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Lin X, Kapoor A, Gu Y et al (2020) Contributions of DNA damage to Alzheimer’s disease. Int J Mol Sci 21(5):1666. https://doi.org/10.3390/ijms21051666

    Article  CAS  PubMed Central  Google Scholar 

  42. Sferra A, Nicita F, Bertini E (2020) Microtubule dysfunction: a common feature of neurodegenerative diseases. Int J Mol Sci 21(19):7354. https://doi.org/10.3390/ijms21197354

    Article  CAS  PubMed Central  Google Scholar 

  43. Frade JM, Gage FH (eds) (2017) Genomic mosaicism in neurons and other cell types. Springer, New York

    Google Scholar 

  44. Gupta P, Balasubramaniam N, Chang HY et al (2020) A single-neuron: current trends and future prospects. Cell 9(6):1528. https://doi.org/10.3390/cells9061528

    Article  Google Scholar 

  45. Dai X, Guo X (2021) Decoding and rejuvenating human ageing genomes: lessons from mosaic chromosomal alterations. Ageing Res Rev 68:101342. https://doi.org/10.1016/j.arr.2021.101342

    Article  CAS  PubMed  Google Scholar 

  46. Yurov YB, Vorsanova SG, Liehr T et al (2014) X chromosome aneuploidy in the Alzheimer’s disease brain. Mol Cytogenet 7(1):20. https://doi.org/10.1186/1755-8166-7-20. (an open-access article distributed under the terms of the Creative Commons Attribution License).

    Article  PubMed  PubMed Central  Google Scholar 

  47. Bajic VP, Essack M, Zivkovic L et al (2020) The X files: “The mystery of X chromosome instability in Alzheimer’s disease”. Front Genet 10:1368. https://doi.org/10.3389/fgene.2019.01368

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Vorsanova SG, Kolotii AD, Kurinnaia OS et al (2021) Turner’s syndrome mosaicism in girls with neurodevelopmental disorders: a cohort study and hypothesis. Mol Cytogenet 14(1):9. https://doi.org/10.1186/s13039-021-00529-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Hochstenbach R, Buizer-Voskamp JE, Vorstman JA et al (2011) Genome arrays for the detection of copy number variations in idiopathic mental retardation, idiopathic generalized epilepsy and neuropsychiatric disorders: lessons for diagnostic workflow and research. Cytogenet Genome Res 135(3–4):174–202. https://doi.org/10.1159/000332928

    Article  CAS  PubMed  Google Scholar 

  50. Jackson-Cook C (2011) Constitutional and acquired autosomal aneuploidy. Clin Lab Med 31(4):481–511., vii. https://doi.org/10.1016/j.cll.2011.08.002

    Article  PubMed  PubMed Central  Google Scholar 

  51. Graham EJ, Vermeulen M, Vardarajan B et al (2019) Somatic mosaicism of sex chromosomes in the blood and brain. Brain Res 1721:146345. https://doi.org/10.1016/j.brainres.2019.146345

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Vorsanova SG, Iourov IY, Kolotii AD et al (2010) Chromosomal mosaicism in spontaneous abortions: analysis of 650 cases. Russ J Genet 46:1197–1200. https://doi.org/10.1134/S1022795410100133

    Article  CAS  Google Scholar 

  53. Yurov YB, Vorsanova SG, Demidova IA et al (2018) Mosaic brain aneuploidy in mental illnesses: an association of low-level post-zygotic aneuploidy with schizophrenia and comorbid psychiatric disorders. Curr Genomics 19(3):163–172. https://doi.org/10.2174/1389202918666170717154340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Mareschal S, Palau A, Lindberg J et al (2021) Challenging conventional karyotyping by next-generation karyotyping in 281 intensively treated patients with AML. Blood Adv 5(4):1003–1016. https://doi.org/10.1182/bloodadvances.2020002517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Iourov IY, Vorsanova SG, Pellestor F et al (2006) Brain tissue preparations for chromosomal PRINS labeling. Methods Mol Biol 334:123–132. https://doi.org/10.1385/1-59745-068-5:123

    Article  PubMed  Google Scholar 

  56. Yurov YB, Vorsanova SG, Soloviev IV et al (2017) FISH-based assays for detecting genomic (chromosomal) mosaicism in human brain cells. NeuroMethods 131:27–41. https://doi.org/10.1007/978-1-4939-7280-7_2

    Article  CAS  Google Scholar 

  57. Iourov IY, Soloviev IV, Vorsanova SG et al (2005) An approach for quantitative assessment of fluorescence in situ hybridization (FISH) signals for applied human molecular cytogenetics. J Histochem Cytochem 53(3):401–408. https://doi.org/10.1369/jhc.4A6419.2005

    Article  CAS  PubMed  Google Scholar 

  58. Vorsanova SG, Iourov IY, Beresheva AK et al (2005) Non-disjunction of chromosome 21, alphoid DNA variation, and sociogenetic features of Down syndrome. Tsitol Genet 39(6):30–36

    CAS  PubMed  Google Scholar 

  59. Iourov IY (2017) Quantitative fluorescence in situ hybridization (QFISH). Methods Mol Biol 1541:143–149. https://doi.org/10.1007/978-1-4939-6703-2_13

    Article  CAS  PubMed  Google Scholar 

  60. Amakawa G, Ikemoto K, Ito H et al (2013) Quantitative analysis of centromeric FISH spots during the cell cycle by image cytometry. J Histochem Cytochem 61(10):699–705. https://doi.org/10.1369/0022155413498754

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. van den Bos H, Spierings DC, Taudt AS et al (2016) Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer’s disease neurons. Genome Biol 17(1):116. https://doi.org/10.1186/s13059-016-0976-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Ye CJ, Stilgenbauer L, Moy A et al (2019) What is karyotype coding and why is genomic topology important for cancer and evolution? Front Genet 10:1082. https://doi.org/10.3389/fgene.2019.01082

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

The help of Dr. Oxana S. Kurinnaia is acknowledged. This work was partially supported by RFBR and CITMA according to the research project no. 18–515-34005. Vorsanova’s lab was supported by the Government Assignment of the Russian Ministry of Health, Assignment 121031000238-1. Yurov's lab was supported by the Government Assignment of the Russian Ministry of Science and Higher Education, Assignment AAAA-A19–119040490101-6.

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Yurov, Y.B., Vorsanova, S.G., Iourov, I.Y. (2023). FISHing for Chromosome Instability and Aneuploidy in the Alzheimer’s Disease Brain. In: Chun, J. (eds) Alzheimer’s Disease. Methods in Molecular Biology, vol 2561. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2655-9_10

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  • DOI: https://doi.org/10.1007/978-1-0716-2655-9_10

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