Human Genetics

, Volume 129, Issue 3, pp 295–305 | Cite as

Transcriptomic analysis of cell-free fetal RNA suggests a specific molecular phenotype in trisomy 18

  • Keiko Koide
  • Donna K. Slonim
  • Kirby L. Johnson
  • Umadevi Tantravahi
  • Janet M. Cowan
  • Diana W. Bianchi
Original Investigation


Trisomy 18 is a common human aneuploidy that is associated with significant perinatal mortality. Unlike the well-characterized “critical region” in trisomy 21 (21q22), there is no corresponding region on chromosome 18 associated with its pathogenesis. The high morbidity and mortality of affected individuals has limited extensive investigations. In order to better understand the molecular mechanisms underlying the congenital anomalies observed in this condition, we investigated the in utero gene expression profile of second trimester fetuses affected with trisomy 18. Total RNA was extracted from cell-free amniotic fluid supernatant from aneuploid fetuses and euploid controls matched for gestational age and hybridized to Affymetrix U133 Plus 2.0 arrays. Individual differentially expressed transcripts were obtained by two-tailed t tests. Over-represented functional pathways among these genes were identified with DAVID and Ingenuity® Pathways Analysis. Results show that three hundred and fifty-two probe sets representing 251 annotated genes were statistically significantly differentially expressed between trisomy 18 and controls. Only 7 genes (2.8% of the annotated total) were located on chromosome 18, including ROCK1, an up-regulated gene involved in valvuloseptal and endocardial cushion formation. Pathway analysis indicated disrupted function in ion transport, MHCII/T cell mediated immunity, DNA repair, G-protein mediated signaling, kinases, and glycosylation. Significant down-regulation of genes involved in adrenal development was identified, which may explain both the abnormal maternal serum estriols and the pre and postnatal growth restriction in trisomy 18. Comparison of this gene set to one previously generated for trisomy 21 fetuses revealed only six overlapping differentially regulated genes. This study contributes novel information regarding functional developmental gene expression differences in fetuses with trisomy 18.


Ingenuity Pathway Analysis Endocardial Cushion Edwards Syndrome Trimester Fetus Ingenuity Pathway Analysis Network 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The project described was supported by Award Number R01 HD 042053-07 from the Eunice Kennedy Shriver National Institute of Child Health & Human Development (to DWB). The content is solely the responsibility of the authors and does not necessarily represent the official views of the Eunice Kennedy Shriver National Institute of Child Health & Human Development or the National Institutes of Health. The work was also supported by National Institutes of Health grant R01 HD 058880-01 (to DKS). The authors have no conflicts of interest to disclose.

Supplementary material

439_2010_923_MOESM1_ESM.doc (480 kb)
Supplementary material 1 (DOC 480 kb)


  1. Altug-Teber Ö, Walter M, Mau-Holzmann UA, Dufke A, Stappert H, Tekesin I, Heilbronner H, Nieselt K, Riess O (2007) Specific transcriptional changes in human fetuses with autosomal trisomies. Cytogenet Genome Res 119:171–184CrossRefPubMedGoogle Scholar
  2. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM, InterPro Consortium (2000) InterPro: an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16:1145–1150CrossRefPubMedGoogle Scholar
  3. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29CrossRefPubMedGoogle Scholar
  4. Barker WC, Garavelli JS, Huang H, McGarvey PB, Orcutt BC, Srinivasarao GY, Xiao C, Yeh LS, Ledley RS, Janda JF, Pfeiffer F, Mewes HW, Tsugita A, Wu C (2000) The protein information resource (PIR). Nucleic Acids Res 28:41–44CrossRefPubMedGoogle Scholar
  5. Baty BJ, Blackburn BL, Carey JC (1994a) Natural history of trisomy 18 and trisomy 13: I. Growth, physical assessment, medical histories, survival, and recurrence risk. Am J Med Genet 49:175–188CrossRefPubMedGoogle Scholar
  6. Baty BJ, Jorde LB, Blackburn BL, Carey JC (1994b) Natural history of trisomy 18 and trisomy 13: II. Psychomotor development. Am J Med Genet 49:189–194CrossRefPubMedGoogle Scholar
  7. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc Ser B 57:289–300Google Scholar
  8. Bettio D, Levi Setti P, Bianchi P, Grazioli V (2003) Trisomy 18 mosaicism in a woman with normal intelligence. Am J Med Genet A 120A:303–304CrossRefPubMedGoogle Scholar
  9. Dennis G Jr., Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4A:P3CrossRefGoogle Scholar
  10. Edwards JH, Harnden DG, Cameron AH, Crosse VM, Wolf OH (1960) A new trisomic syndrome. Lancet 275:787–789CrossRefGoogle Scholar
  11. Embleton ND, Wyllie JP, Wright MJ, Burn J, Hunter S (1996) Natural history of trisomy 18. Arch Dis Child 75:F38–F41Google Scholar
  12. Gentleman R, Carey V, Huber W, Irizarry RA, Duduoit S (2005) Bioinformatics and computational biology solutions Using R and bioconductor. Springer Press, New YorkCrossRefGoogle Scholar
  13. Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57CrossRefPubMedGoogle Scholar
  14. Hui L, Bianchi DW (2010) Cell-free fetal nucleic acids in amniotic fluid. Hum Reprod Update (Oct 5 epub ahead of print)Google Scholar
  15. Ichizaki T, Maekawa M, Fujisawa K, Okawa K, Iwamatsu A, Fujita A, Watanabe N, Saito Y, Kakizuka A, Morii N, Narumiya S (1996) The small GTP-binding protein Rho binds to and activates a 160 kDa Ser/Thr protein kinase homologous to myotonic dystrophy kinase. EMBO J 15:1885–1893Google Scholar
  16. Irons M, Elias ER, Salen G, Tint GS, Batta AK (1993) Defective cholesterol biosynthesis in Smith-Lemli-Opitz syndrome. Lancet 341:1414CrossRefPubMedGoogle Scholar
  17. Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28:27–30CrossRefPubMedGoogle Scholar
  18. Kempná P, Flück CE (2008) Adrenal gland development and defects. Best Pract Res Clin Endocrinol Metab 22:77–93CrossRefPubMedGoogle Scholar
  19. Kohn G, Shohat M (1987) Trisomy 18 mosaicism in an adult with normal intelligence. Am J Med Genet 26:929–931CrossRefPubMedGoogle Scholar
  20. Korenberg JR, Kawashima H, Pulst SM, Ikeuchi T, Ogasawara N, Yamamoto K, Schonberg SA, West R, Allen L, Magenis E, Ikawa K, Taniguchi N, Epstein CJ (1990) Molecular definition of a region of chromosome 21 that causes features of the Down syndrome phenotype. Am J Hum Genet 47:236–246PubMedGoogle Scholar
  21. Kourie JI (1998) Interaction of reactive oxygen species with ion transport mechanisms. Am J Physiol 275:C1–C4PubMedGoogle Scholar
  22. Lam WW, Kirk J, Manning N, Reardon W, Kelley RI, Fitzpatrick D (2006) Decreased cholesterol synthesis as a possible aetiological factor in malformations of trisomy 18. Eur J Med Genet 49:195–199CrossRefPubMedGoogle Scholar
  23. Langlois D, Li JY, Saez JM (2002) Development and function of the human fetal adrenal cortex. J Pediatr Endocrinol Metab 15(Suppl 5):1311–1322PubMedGoogle Scholar
  24. Leung T, Manser E, Tan L, Lim L (1985) A novel serine/threonine kinase binding the Ras-related RhoA GTPase which translocates the kinase to peripheral membranes. J Biol Chem 270:29051–29054Google Scholar
  25. Makrydimas G, Plachouras N, Thilaganathan B, Nicolaides KH (1994) Abnormal immunological development in fetuses with trisomy 18. Prenat Diagn 14:239–241CrossRefPubMedGoogle Scholar
  26. Matsui T, Amano M, Yamamoto T, Chihara K, Nakafuku M, Ito M, Nakano T, Okawa K, Iwamatsu A, Kaibuchi K (1996) Rho-associated kinase, a novel serine/threonine kinase, as a putative target for small GTP binding protein Rho. EMBO J 15:2208–2216PubMedGoogle Scholar
  27. Matsuoka R, Matsuyama S, Yamamoto Y, Kuroki Y, Matsui I (1981) Trisomy 18q: a case report and review of karyotype–phenotype correlations. Hum Genet 57:78–82CrossRefPubMedGoogle Scholar
  28. Mewar R, Kline AD, Harrison W, Rojas K, Greenberg F, Overhauser J (1993) Clinical and molecular evaluation of four patients with partial duplications of the long arm of chromosome 18. Am J Hum Genet 53:1269–1278PubMedGoogle Scholar
  29. Mootha V, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstråle M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC (2003) PGC-1 alpha-responsive genes involved in oxidative phosphorylation are coordinately down-regulated in human diabetes. Nat Genet 34:267–273CrossRefPubMedGoogle Scholar
  30. Morris JK, Savva GM (2008) The risk of fetal loss following a prenatal diagnosis of trisomy 13 or trisomy 18. Am J Med Genet A 46A:827–832Google Scholar
  31. Rasmussen SA, Wong LY, Yang Q, May KM, Friedman JM (2003) Population-based analyses of mortality in trisomy 13 and 18. Pediatrics 111:777–784CrossRefPubMedGoogle Scholar
  32. Sakabe M, Ikeda K, Nakatani K, Kawada N, Imanaka-Yoshida K, Yoshida T, Yamagishi T, Nakajima Y (2006) Rho kinases regulate endothelial invasion and migration during valvuloseptal endocardial cushion tissue formation. Dev Dyn 235:94–104CrossRefPubMedGoogle Scholar
  33. Sakabe M, Sakata H, Matsui H, Ikeda K, Yamagishi T, Nakajima Y (2008) ROCK1 expression is regulated by TGFbeta3 and ALK2 during valvuloseptal endocardial cushion formation. Anat Rec 291:845–857CrossRefGoogle Scholar
  34. Shapiro BL (1997) Whither Down syndrome critical regions? Hum Genet 99:421–423CrossRefPubMedGoogle Scholar
  35. Slonim DK, Koide K, Johnson KL, Tantravahi U, Cowan JM, Jarrah Z, Bianchi DW (2009) Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses. Proc Natl Acad Sci USA 106:9425–9429CrossRefPubMedGoogle Scholar
  36. Smith DW, Patau K, Therman E, Inhorn SL (1960) A new autosomal trisomy syndrome: multiple congenital anomalies caused by an extra chromosome. J Pediatr 57:338–345CrossRefPubMedGoogle Scholar
  37. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545–15550CrossRefPubMedGoogle Scholar
  38. Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechanie A (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 13:2129–2141CrossRefPubMedGoogle Scholar
  39. Turcan S, Slonim D, Vetter D (2010) Lack of nAChr activity depresses cochlear maturation and up-regulates GABA system components: temporal profiling of gene expression in alpha9-null mice. PLoS One 5:e9058CrossRefPubMedGoogle Scholar
  40. Turleau C, de Grouchy J (1977) Trisomy 18qter and trisomy mapping of chromosome 18. Clin Genet 12:361–371CrossRefPubMedGoogle Scholar
  41. Turner M, O’Herlihy C (1984) Adrenal hypofunction and trisomy 18. Obstet Gynecol 6(Suppl 3):84–95Google Scholar
  42. Van Dyke DC, Allen M (1990) Clinical management in long-term survivors with trisomy 18. Pediatrics 85:753–759PubMedGoogle Scholar
  43. Zhao Z, Rivkees SA (2004) Rho-associated kinases play a role in endocardial cell differentiation and migration. Devel Biol 275:183–191CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Keiko Koide
    • 1
  • Donna K. Slonim
    • 2
  • Kirby L. Johnson
    • 1
  • Umadevi Tantravahi
    • 3
  • Janet M. Cowan
    • 1
  • Diana W. Bianchi
    • 1
  1. 1.Division of Genetics, Department of PediatricsFloating Hospital for Children at Tufts Medical CenterBostonUSA
  2. 2.Department of Computer ScienceTufts University School of EngineeringMedfordUSA
  3. 3.Department of PathologyWomen and Infants’ HospitalProvidenceUSA

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