Cytogenomics and epileptology: a desired alliance
https://doi.org/10.56618/2071-2693_2023_15_4_147
EDN: DLTESL
Abstract
Since 2021, theoretical studies in the framework of a collaboration between researchers of Mental Health Research Center (and Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University) and Polenov Neurosurgical Institute, Almazov National Medical Research Centre have resulted in the formation of a consortium designated as “Cytogenomic epileptology”. Here, the work of the consortium is described; the essential problems, which are planned to be solved by our consortium members, are listed. More specifically, chromosomal abnormalities and copy number variants are insufficiently studied in epileptic disorders; these types of genetic pathology are excluded from current epilepsy classification; analyses of intraoperational (postoperational) samples are limited to searching gene mutations; systems genomics is rarely used for uncovering epilepsy pathogenesis. It is planned to invite additional consortium members according to selection criteria.
Keywords
About the Authors
I. Y. IourovRussian Federation
Ivan Yu. Iourov.
Moscow
A. P. Gerasimov
Russian Federation
Alexandr P. Gerasimov.
Saint Petersburg
O. S. Kurinnaia
Russian Federation
Oksana S. Kurinnaia.
Moscow
N. E. Ivanova
Russian Federation
Natalya E. Ivanova.
Saint Petersburg
I. A. Demidova
Russian Federation
Irina A. Demidova.
Moscow
Y. M. Zabrodskaya
Russian Federation
Yulia M. Zabrodskaya.
Saint Petersburg
K. K. Kukanov
Russian Federation
Konstantin K. Kukanov.
Saint Petersburg
A. D. Kolotii
Russian Federation
Alexey D. Kolotii.
Moscow
K. S. Vasin
Russian Federation
Kirill S. Vasin.
Moscow
S. G. Vorsanova
Russian Federation
Svetlana G. Vorsanova.
Moscow
K. A. Samochernyh
Russian Federation
Konstantin A. Samochernyh.
Saint Petersburg
References
1. Iourov IY, Gerasimov AP, Zelenova MA, Ivanova NE, Kurinnaia OS, Zabrodskaya YM, Demidova IA, Barantsevich ER, Vasin KS, Kolotii AD, Ushanov VV, Sitovskaya DA, Lobzhanidze TB, Iuditskaia ME, Iakushev NS, Zhumatov MM, Vorsanova SG, Samochernyh KA. Cytogenomic epileptology. Mol Cytogenet. 2023;16:1. https://doi.org/10.1186/s13039–022–00634-w
2. Perucca P, Bahlo M, Berkovic SF. The genetics of epilepsy. Annu Rev Genom Hum Genet. 2020;21:205–30. https://doi.org/10.1146/annurev-genom-120219–074937
3. Iourov I.Y., Vorsanova S. G., Yurov Y. B. Pathway-based classification of genetic diseases. Mol Cytogenet. 2019;12:4. https://doi.org/10.1186/s13039-019-0418-4
4. Savojardo C, Baldazzi D, Babbi G, Martelli PL, Casadio R. Mapping human disease-associated enzymes into Reactome allows characterization of disease groups and their interactions. Sci Rep. 2022;12(1):17963. https://doi.org/10.1038/s41598-022-22818-5
5. McMahon JM, Scheffer IE, Nicholl JK, Waters W, Eyre H, Hinton L, Nelson P, Yu S, Dibbens LM, Berkovic SF, Mulley JC. detection of microchromosomal aberrations in refractory epilepsy: a pilot study. Epileptic Disord. 2010;12(3):192–8. https://doi.org/10.1684/epd.2010.0326
6. Niestroj LM, Perez-Palma E, Howrigan DP, Zhou Y, Cheng F, Saarentaus E, Nürnberg P, Stevelink R, Daly MJ, Palotie A, Lal D, Epi25 Collaborative. Epilepsy subtype-specific copy number burden observed in a genome-wide study of 17 458 subjects. Brain. 2020;143(7):2106–18. https://doi.org/10.1093/brain/awaa171.
7. Iourov I.Y., Vorsanova S.G., Yurov Y. B. The variome concept: focus on CNVariome. Mol Cytogenet. 2019;12:52. https://doi.org/10.1186/s13039-019-0467-8
8. Iourov I.Y., Vorsanova S. G., Yurov Y. B. Modern achievements in molecular cytogenetic diagnosis of hereditary diseases. Clinical laboratory diagnosis. 2005;№ 11:21–29. (In Russ.).
9. Mulley JC, Mefford HC. Epilepsy and the new cytogenetics. Epilepsia. 2011;52(3):423–32. https://doi.org/10.1111/j.1528–1167.2010.02932.x
10. Iourov I.Y., Vorsanova S. G., Yurov Y. B. Single cell genomics of the brain: focus on neuronal diversity and neuropsychiatric diseases. Curr Genomics. 2012; 13(6):477–488. https://doi.org/10.2174/138920212802510439
11. Heng E, Thanedar S, Heng HH. Challenges and opportunities for clinical cytogenetics in the 21st century. Genes (Basel). 2023;14(2):493. https://doi.org/10.3390/genes14020493
12. Iourov I. Y., Vorsanova S. G., Yurov Y. B. In silico molecular cytogenetics: a bioinformatic approach to prioritization of candidate genes and copy number variations for basic and clinical genome research. Mol Cytogenet. 2014;7(1):98. https://doi.org/10.1186/s13039–014–0098-z
13. Yang MQ, Yoshigoe K, Yang W, Tong W, Qin X, Dunker A, Chen Z, Arbania HR, Liu JS, Niemierko A, Yang JY. The emerging genomics and systems biology research lead to systems genomics studies. BMC Genomics. 2014;15 Suppl 11(Suppl 11): I1. https://doi.org/10.1186/1471–2164–15-S11-I1
14. Noebels J. pathway-driven discovery of epilepsy genes. Nat Neurosci. 2015;18(3):344–50. https://doi.org/10.1038/nn.3933.
15. Iourov I. Y., Vorsanova S. G., Yurov Y. B. Systems cytogenomics: are we ready yet? Curr Genomics. 2021;22(2):75–78. https://doi.org/10.2174/1389202922666210219112419
16. Heng HH, Horne SD, Chaudhry S, Regan SM, Liu G, Abdallah BY, Ye CJ. A postgenomic perspective on molecular cytogenetics. Curr Genomics. 2018;19(3):227–239. https://doi.org/10.2174/1389202918666170717145716
17. Schaffer LV, Ideker T. Mapping the multiscale structure of biological systems. Cell Syst. 2021;12(6):622–635. https://doi.org/10.1016/j.cels.2021.05.012
18. Iourov I.Y., Vorsanova S. G., Voinova V.Y., Yurov Y. B. 3p22.1p21.31 microdeletion identifies CCK as Asperger syndrome candidate gene and shows the way for therapeutic strategies in chromosome imbalances. Mol Cytogenet. 2015;8:82. https://doi.org/10.1186/s13039-015-0185-9
19. Iourov I.Y., Vorsanova S. G., Korostelev S.A., Zelenova M.A., Yurov Y. B. Long contiguous stretches of homozygosity spanning shortly the imprinted loci are associated with intellectual disability, autism and/or epilepsy. Mol Cytogenet. 2015;8:77. https://doi.org/10.1186/s13039–015–0182-z
20. Wang TS, Tsai WH, Tsai LP, Wong SB. Clinical characteristics and epilepsy in genomic imprinting disorders: Angelman syndrome and prader-willi syndrome. Ci Ji Yi Xue Za Zhi. 2019;32(2):137–44. https://doi.org/10.4103/tcmj.tcmj_103_19.
21. Iourov I.Y., Vorsanova S. G., Yurov Y. B., Kutsev S. I. Ontogenetic and pathogenetic views on somatic chromosomal mosaicism. Genes. 2019;10(5):379. https://doi.org/10.3390/genes10050379
22. Ye Z, Mcquillan L, Poduri A, Green TE, Matsumoto N, Mefford HC, Scheffer IE, Berkovic SF, Hildebrand MS. Somatic mutation: the hidden genetics of brain malformations and focal epilepsies. Epilepsy Res. 2019;155:106161. https://doi.org/10.1016/j.eplepsyres.2019.106161
23. Costantino I, Nicodemus J, Chun J. Genomic mosaicism formed by somatic variation in the aging and diseased brain. Genes (Basel). 2021;12(7):1071. doi: https://doi.org/10.3390/genes12071071
24. Iourov IY, Vorsanova SG, Kurinnaia OS, Kutsev SI, Yurov YB. Somatic mosaicism in the diseased brain. Mol Cytogenet. 2022;15:45. https://doi.org/10.1186/s13039–022–00624-y
25. Iourov I. Y., Vorsanova S. G., Yurov Y. B., Zelenova M. A., Kurinnaia O. S., Vasin K. S., Kutsev S. I. The The cytogenomic «theory of everything»: chromohelkosis may underlie chromosomal instability and mosaicism in disease and aging. Int J Mol Sci. 2020;21(21):8328. https://doi.org/10.3390/ijms21218328
26. Albert O, Sun S, Huttner A, Zhang Z, Suh Y, Campisi J, Vijg J, Montagna C. Chromosome instability and aneuploidy in the mammalian brain. Chromosome Res. 2023;31(4):32. https://doi.org/10.1007/s10577–023–09740-w
27. Mullen SA, Berkovic SF. ILAE Genetics Commission. Genetic generalized epilepsies. Epilepsia. 2018;59(6):1148–53. https://doi.org/10.1111/epi.14042
28. Krey I, Platzer K, Esterhuizen A, Berkovic SF, Helbig I, Hildebrand MS, Lerche H, Lowenstein D, Møller RS, Poduri A, Sadleir L, Sisodiya SM, Weckhuysen S, Wilmshurst JM, Weber Y, Lemke JR, Berkovic SF, Cross JH, Helbig I, Lerche H, Lowenstein D, Mefford HC, Perucca P, Tan NC, Caglayan H, Helbig K, Singh G, Weber Y, Weckhuysen S. Current practice in diagnostic genetic testing of the epilepsies. Epileptic Disord. 2022;24(5):765–86. https://doi.org/10.1684/epd.2022
29. Rastin C, Schenkel LC, Sadikovic B. Complexity in genetic epilepsies: a comprehensive review. Int J Mol Sci. 2023;24(19):14606. https://doi.org/10.3390/ijms241914606
30. Iourov IY, Vorsanova SG. Yuri B. Yurov (1951–2017). Mol Cytogenet. 2018;11:36. https://doi.org/10.1186/s13039-018-0383-3.
Review
For citations:
Iourov I.Y., Gerasimov A.P., Kurinnaia O.S., Ivanova N.E., Demidova I.A., Zabrodskaya Y.M., Kukanov K.K., Kolotii A.D., Vasin K.S., Vorsanova S.G., Samochernyh K.A. Cytogenomics and epileptology: a desired alliance. Russian Neurosurgical Journal named after Professor A. L. Polenov. 2023;15(4):147-151. (In Russ.) https://doi.org/10.56618/2071-2693_2023_15_4_147. EDN: DLTESL