Current possibilities of transcriptomics in the study of preeclampsia

1. Law K.P., Han T.L., Tong C., Baker P.N. Mass spectrometry-based proteomics for pre-eclampsia and preterm birth. Int. J. Mol. Sci. 2015; 16(5): 10952-85. https://dx.doi.org/10.3390/ijms160510952.
2. Napso T., Zhao X., Lligoña M.I., Sandovici I., Kay R.G., George A.L. et al. Placental secretome characterization identifies candidates for pregnancy complications. Commun. Biol. 2021; 4(1): 701. https://dx.doi.org/10.1038/s42003-021-02214-x.
3. Прокопенко В.М. Применение протеомного анализа в акушерстве (первые результаты исследований). Российский вестник акушера-гинеколога. 2016; 16(1): 28-32. https://dx.doi.org/10.17116/rosakush201616128-32. [Prokopenko V.M. Use of proteomic analysis in obstetrics: First results of investigations. Russian Bulletin of Obstetrician-Gynecologist. 2016; 16(1): 28 32. (in Russian)]. https://dx.doi.org/10.17116/rosakush201616128-32.
4. NCBI MeSH (электронный ресурс). Available at: http://www. ncbi.nlm.nih.gov/mesh
5. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009; 10(1): 57-63.https://dx.doi.org/10.1038/nrg2484.
6. Calvel P., Rolland A.D., Jégou B., Pineau C. Testicular postgenomics: targeting the regulation of spermatogenesis. Philos. Trans. R Soc. Lond. B Biol. Sci. 2010; 365(1546): 1481-500. https://dx.doi.org/10.1098/rstb.2009.0294.
7. Yong H.E.J., Chan S.Y. Current approaches and developments in transcript profiling of the human placenta. Hum. Reprod. Update. 2020; 26(6): 799-840. https://dx.doi.org/10.1093/humupd/dmaa028.
8. Sánchez-Pla A., Reverter F., Ruíz de Villa M.C., Comabella M. Transcriptomics: mRNA and alternative splicing. J. Neuroimmunol. 2012; 248(1-2): 23-31. https://dx.doi.org/10.1016/j.jneuroim.2012.04.008.
9. Leavey K., Bainbridge S.A., Cox B.J. Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia. PLoS One. 2015; 10(2): e0116508. https://dx.doi.org/10.1371/journal.pone.0116508.
10. Liu S., Wang Z., Zhu R., Wang F., Cheng Y., Liu Y. Three differential expression analysis methods for RNA sequencing: limma, EdgeR, DESeq2. J. Vis. Exp. 2021 Sep 18; (175). https://dx.doi.org/10.3791/62528.
11. Клинические рекомендации. Преэклампсия. Эклампсия. Отеки, протеинурия и гипертензивные расстройства во время беременности, в родах и послеродовом периоде М.: Российское общество акушеров-гинекологов; Ассоциация анестезиологов-реаниматологов; Ассоциация акушерских анестезиологов-реаниматологов. 2021. [Preeclampsia. Eclampsia. Edema, proteinuria and hypertensive disorders during pregnancy, childbirth and the postpartum period (Clinical guidelines). M.; 2021. (in Russian)].
12. World Health Organization. WHO recommendations for prevention, treatment of pre-eclampsia, and eclampsia. 2014. Available at: https://preeclampsia.org/frontend/assets/img/advocacy_resource/9789241548335_eng_1579174434.pdf
13. Ukah V., De Silva D.A., Payne B. Prediction of adverse maternal outcomes from pre-eclampsia and other hypertensive disorders of pregnancy: A systematic review. Pregnancy Hypertens. 2017; 11: 115-23. https://dx.doi.org/10.1016/j.preghy.2017.11.006.
14. Щеголев А.И., Туманова У.Н., Шувалова М.П., Фролова О.Г. Гипоксия как причина мертворождаемости в Российской Федерации. Здоровье, демография, экология финно-угорских народов. 2014; 3: 96-8. [Shchegolev A.I, Tumanova U.N., Shuvalova M.P., Frolova O.G. Hypoxia as a cause of stillbirth in the Russian Federation. Health, demography, ecology of Finno-Ugric peoples. 2014; 3: 96-8. (in Russian)].
15. Gong S., Gaccioli F., Dopierala J., Sovio U., Cook E., Volders P., Martens L. et al. The RNA landscape of the human placenta in health and disease. Nat. Commun. 2021; 12(1): 2639. https://doi.org/10.1038/s41467-021-22695-y.
16. Щеголев А.И., Туманова У.Н., Ляпин В.М., Серов В.Н. Синцитиотрофобласт ворсин плаценты в норме и при преэклампсии. Акушерство и гинекология. 2020; 6: 21-8. https://dx.doi.org/10.18565/aig.2020.6.21-28. [Shchegolev A.I., Tumanova U.S., Lyapin V.M., Serov V.N. The syncytiotrophoblast of the placental villi in health and in preeclampsia. Obstetrics and Gynecology. 2020; 6; 21-8. (in Russian)]. https://dx.doi.org/10.18565/aig.2020.6.21-28.
17. Szilagyi A., Gelencser Z., Romero R., Xu Y., Kiraly P., Demeter A. et al. Placenta-specific genes, their regulation during villous trophoblast differentiation and dysregulation in preterm preeclampsia. Int. J. Mol. Sci. 2020; 21(2): 628.https://dx.doi.org/10.3390/ijms21020628.
18. Ellery P.M., Cindrova-Davies T., Jauniaux E., Ferguson-Smith A.C., Burton G.J. Evidence for transcriptional activity in the syncytiotrophoblast of the humanplacenta. Placenta. 2009; 30(4): 329-34. https://dx.doi.org/10.1016/j.placenta.2009.01.002.
19. Lim Y.C., Li J., Ni Y., Liang Q., Zhang J., Yeo G.S.H. et al. A complex association between DNA methylation and gene expression in human placenta at first and third trimesters. PLoS One. 2017; 12(7): e0181155.https://dx.doi.org/10.1371/journal. pone.0181155.
20. Leavey K., Benton S.J., Grynspan D., Bainbridge S.A., Morgen E.K., Cox B.J. Gene markers of normal villous maturation and their expression in placentas with maturational pathology. Placenta. 2017; 58: 52-9. https://dx.doi.org/10.1016/j.placenta.2017.08.005.
21. Wang B., Wang P., Parobchak N., Treff N., Tao X., Wang J., Rosen T. Integrated RNA-seq and ChIP-seq analysis reveals a feed-forward loop regulating H3K9ac and key labor drivers in human placenta. Placenta. 2019; 76: 40-50.https://dx.doi.org/10.1016/j.placenta.2019.01.010.
22. Cvitic S., Longtine M.S., Hackl H., Wagner K., Nelson M.D., Desoye G., Hiden U. The human placental sexome differs between trophoblast epithelium and villous vessel endothelium. PLoS One. 2013; 8(10): e79233.https://dx.doi.org/10.1371/journal.pone.0079233.
23. Than N.G., Romero R., Tarca A.L., Kekesi K.A., Xu Y., Xu Z. et al. Integrated systems biology approach identifies novel maternal and placental pathways of preeclampsia. Front. Immunol. 2018; 9: 1661. https://dx.doi.org/10.3389/fimmu.2018.01661.
24. Soncin F., Natale D., Parast M.M. Signaling pathways in mouse and human trophoblast differentiation: a comparative review. Cell. Mol. Life Sci. 2015; 72(7): 1291-302. https://dx.doi.org/10.1007/s00018-014-1794-x.
25. Meyer zu Schwabedissen H.E., Grube M., Dreisbach A., Jedlitschky G., Meissner K., Linneman K. et al. Epidermal growth factor-mediated activation of the map kinase cascade results in altered expression and function of ABCG2 (BCRP). Drug Metab. Dispos. 2006; 34(4): 524-33. https://dx.doi.org/10.1124/dmd.105.007591.
26. Prast J., Saleh L., Husslein H., Sonderegger S., Helmer H., Knöfler M. Human chorionic gonadotropin stimulates trophoblast invasion through extracellularly regulated kinase and AKT signaling. Endocrinology. 2008; 149(3): 979-87. https://dx.doi.org/10.1210/en.2007-1282.
27. Luo Y., Kumar P., Mendelson C.R. Estrogen-related receptor γ (ERRγ) regulates oxygen-dependent expression of voltage-gated potassium (K+) channels and tissue kallikrein during human trophoblast differentiation. Mol. Endocrinol. 2013; 27(6): 940-52. https://dx.doi.org/10.1210/me.2013-1038.
28. Paul S., Home P., Bhattacharya B., Ray S. GATA factors: Master regulators of gene expression in trophoblast progenitors. Placenta. 2017; 60(Suppl. 1): S61-6. https://dx.doi.org/10.1016/j.placenta.2017.05.005.
29. Vaiman D., Miralles F. An integrative analysis of preeclampsia based on the construction of an extended composite network featuring protein-protein physical interactions and transcriptional relationships. PLoS One. 2016; 11(11): e0165849. https://dx.doi.org/10.1371/journal.pone.0165849.
30. Wang A., Rana S., Karumanchi S.A. Preeclampsia: the role of angiogenic factors in its pathogenesis. Physiology (Bethesda). 2009; 24: 147-58.https://dx.doi.org/10.1152/physiol.00043.2008.
31. Louwen F., Muschol-Steinmetz C., Reinhard J., Reitter A., Yuan J. A lesson for cancer research: placental microarray gene analysis in preeclampsia. Oncotarget. 2012; 3(8): 759-73. https://dx.doi.org/10.18632/oncotarget.595.
32. Kaartokallio T., Cervera A., Kyllönen A., Laivuori K., Kere J., Laivuori H.; FINNPEC Core Investigator Group. Gene expression profiling of pre-eclamptic placentae by RNA sequencing. Sci. Rep. 2015; 5: 14107. https://dx.doi.org/10.1038/srep14107.
33. Founds S.A., Conley Y.P., Lyons-Weiler J.F., Jeyabalan A., Hogge W.A., Conrad K.P. Altered global gene expression in first trimester placentas of women destined to develop preeclampsia. Placenta. 2009; 30(1): 15-24.https://dx.doi.org/10.1016/j.placenta.2008.09.015.
34. Tong J., Zhao W., Lv H., Li W.P., Chen Z.J., Zhang C. Transcriptomic profiling in human decidua of severe preeclampsia detected by RNA sequencing. J. Cell. Biochem. 2018; 119(1): 607-15. https://dx.doi.org/10.1002/jcb.26221.
35. Vishnyakova P., Poltavets A., Nikitina M., Muminova K., Potapova A., Vtorushina V., Loginova N., Midiber K., Mikhaleva L., Lokhonina A., Khodzhaeva Z., Pyregov A., Elchaninov A., Fatkhudinov T., Sukhikh G. Preeclampsia: inflammatory signature of decidual cells in early manifestation of disease. Placenta. 2021; 104: 277-83. https://dx.doi.org/10.1016/j.placenta.2021.01.011.
36. Yong H.E., Melton P.E., Johnson M.P., Freed K.A., Kalionis B., Murthi P. et al. Genome-wide transcriptome directed pathway analysis of maternal pre-eclampsia susceptibility genes. PLoS One. 2015; 10(5): e0128230.https://dx.doi.org/10.1371/journal.pone.0128230.
37. Tsang J.C.H., Vong J.S.L., Ji L., Poon L.C.Y., Jiang P., Lui K.O. et al. Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics. Proc. Natl. Acad. Sci. USA. 2017; 114(37): E7786-95. https://dx.doi.org/10.1073/pnas.1710470114.
38. Deyssenroth M.A., Peng S., Hao K., Lambertini L., Marsit C.J., Chen J. Whole-transcriptome analysis delineates the human placenta gene network and its associations with fetal growth. BMC Genomics. 2017; 18(1): 520.https://dx.doi.org/10.1186/s12864-017-3878-0.
39. Verheecke M., Cortès Calabuig A., Finalet Ferreiro J., Brys V., Van Bree R., Verbist G. et al. Genetic and microscopic assessment of the human chemotherapy-exposed placenta reveals possible pathways contributive to fetal growth restriction. Placenta. 2018; 64: 61-70. https://dx.doi.org/10.1016/j.placenta.2018.03.002.
40. Li S., Hu Y.W. Pathogenesis of uteroplacental acute atherosis: An update on current research. Am. J. Reprod. Immunol. 2021; 85(6): e13397.https://dx.doi.org/10.1111/aji.13397.
41. Sitras V., Fenton C., Acharya G. Gene expression profile in cardiovascular disease and preeclampsia: a meta-analysis of the transcriptome based on raw data from human studies deposited in Gene Expression Omnibus. Placenta. 2015; 36(2): 170-8. https://dx.doi.org/10.1016/j.placenta.2014.11.017.
42. Barker D.J., Thornburg K.L. Placental programming of chronic diseases, cancer and lifespan: a review. Placenta. 2013; 34(10): 841-5.https://dx.doi.org/10.1016/j.placenta.2013.07.063.
43. Peng S., Deyssenroth M.A., Di Narzo A.F., Lambertini L., Marsit C.J., Chen J., Hao K. Expression quantitative trait loci (eQTLs) in human placentas suggest developmental origins of complex diseases. Hum. Mol. Genet. 2017; 26(17): 3432-41. https://dx.doi.org/10.1093/hmg/ddx265.
44. Ren Z., Gao Y., Gao Y., Liang G., Chen Q., Jiang S. et al. Distinct placental molecular processes associated with early-onset and late-onset preeclampsia. Theranostics. 2021; 11(10): 5028-44. https://dx.doi.org/10.7150/thno.56141.
45. Yadama A.P., Maiorino E., Carey V.J., McElrath T.F., Litonjua A.A., Loscalzo J., Weiss S.T., Mirzakhani H. Early-pregnancy transcriptome signatures of preeclampsia: from peripheral blood to placenta. Sci. Rep. 2020; 10(1): 17029. https://dx.doi.org/10.1038/s41598-020-74100-1.
46. Rajakumar A., Chu T., Handley D.E., Bunce K.D., Burke B., Hubel C.A., Jeyabalan A., Peters D.G. Maternal gene expression profiling during pregnancy and preeclampsia in human peripheral blood mononuclear cells. Placenta. 2011; 32(1): 70-8. https://dx.doi.org/10.1038/jp.2013.16.
47. Бабовская А.А., Трифонова Е.А., Зарубин А.А., Марков А.В., Степанов В.А. Поиск ключевых генов преэклампсии с помощью интегративного биоинформатического анализа. В кн.: Актуальные вопросы современной медицинской науки и здравоохранения: Материалы V Международной научно-практической конференции молодых ученых и студентов, посвященной 75-летию Победы в Великой Отечественной войне, 90-летию УГМУ и 100-летию медицинского образования на Урале. Екатеринбург, 09–10 апреля 2020 г. 2020; 2: 189-94. [Babovskaya A.A., Trifonova E.A., Zarubin A.A., Markov A.V., Stepanov V.A. Identification of hub genes of preeclampsia by integrated bioinformatics analysis. Topical issues of modern medical science and healthcare: collection of articles of the V International (75 All-Russian) Scientific and Practical Conference. Yekaterinburg, April 09–10, 2020. 2020; 2: 189-94.(in Russian)].

Received 28.03.2022

Accepted 14.06.2022