Human Genetics

, Volume 133, Issue 9, pp 1075–1082 | Cite as

Amniotic fluid RNA gene expression profiling provides insights into the phenotype of Turner syndrome

  • Lauren J. MassinghamEmail author
  • Kirby L. Johnson
  • Thomas M. Scholl
  • Donna K. Slonim
  • Heather C. Wick
  • Diana W. Bianchi
Original Investigation


Turner syndrome is a sex chromosome aneuploidy with characteristic malformations. Amniotic fluid, a complex biological material, could contribute to the understanding of Turner syndrome pathogenesis. In this pilot study, global gene expression analysis of cell-free RNA in amniotic fluid supernatant was utilized to identify specific genes/organ systems that may play a role in Turner syndrome pathophysiology. Cell-free RNA from amniotic fluid of five mid-trimester Turner syndrome fetuses and five euploid female fetuses matched for gestational age was extracted, amplified, and hybridized onto Affymetrix® U133 Plus 2.0 arrays. Significantly differentially regulated genes were identified using paired t tests. Biological interpretation was performed using Ingenuity Pathway Analysis and BioGPS gene expression atlas. There were 470 statistically significantly differentially expressed genes identified. They were widely distributed across the genome. XIST was significantly down-regulated (p < 0.0001); SHOX was not differentially expressed. One of the most highly represented organ systems was the hematologic/immune system, distinguishing the Turner syndrome transcriptome from other aneuploidies we previously studied. Manual curation of the differentially expressed gene list identified genes of possible pathologic significance, including NFATC3, IGFBP5, and LDLR. Transcriptomic differences in the amniotic fluid of Turner syndrome fetuses are due to genome-wide dysregulation. The hematologic/immune system differences may play a role in early-onset autoimmune dysfunction. Other genes identified with possible pathologic significance are associated with cardiac and skeletal systems, which are known to be affected in females with Turner syndrome. The discovery-driven approach described here may be useful in elucidating novel mechanisms of disease in Turner syndrome.


Amniotic Fluid Ingenuity Pathway Analysis Turner Syndrome Amniotic Fluid Sample Ingenuity Pathway Analysis Analysis 
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.



Funding for this study was provided by the Eunice Kennedy Shriver National Institute of Child Health and Human Development [R01 HD42053-10 to DWB and R01 HD058880-04 to DKS].

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

439_2014_1448_MOESM1_ESM.xls (88 kb)
Differentially up-regulated Turner syndrome gene list. (XLS 87 kb)
439_2014_1448_MOESM2_ESM.xls (70 kb)
Differentially down-regulated Turner syndrome gene list. (XLS 69 kb)
439_2014_1448_MOESM3_ESM.xls (18 kb)
Chi square analysis of gene dysregulation distribution. (XLS 18 kb)
439_2014_1448_MOESM4_ESM.xls (38 kb)
Turner syndrome transcriptome organ-specific genes identified by BioGPS. (XLS 38 kb)
439_2014_1448_MOESM5_ESM.xls (37 kb)
Turner syndrome transcriptome top biological functions identified by IPA. (XLS 37 kb)


  1. Bakalov VK, Gutin L, Cheng CM, Zhou J, Sheth P, Shah K, Arepalli S, Vanderhoof V, Nelson LM, Bondy CA (2012) Autoimmune disorders in women with Turner syndrome and women with karyotypically normal primary ovarian insufficiency. J Autoimmun 38:315–321PubMedCentralPubMedCrossRefGoogle Scholar
  2. Bianchi D, Crombleholme T, D’Alton M, Malone F (2010) 45,X (Turner syndrome). In: Fetology: Diagnosis and management of the fetal patient, 2nd edn. McGraw-Hill Companies, New YorkGoogle Scholar
  3. Bierer R, Nitta CH, Friedman J, Codianni S, de Frutos S, Dominguez-Bautista JA, Howard TA, Resta TC, Gonzalez Bosc LV (2011) NFATc3 is required for chronic hypoxia-induced pulmonary hypertension in adult and neonatal mice. Am J Physiol Lung Cell Mol Physiol 301:L872–L880PubMedCentralPubMedGoogle Scholar
  4. Bondy CA (2007) Turner syndrome study group: care of girls and women with Turner syndrome: a guideline of the Turner syndrome study group. J Clin Endocrinol Metab 92:10–25PubMedCrossRefGoogle Scholar
  5. Clarkson PM, Nicholson MR, Barratt-Boyes BG, Neutze JM, Whitlock RM (1983) Results after repair of coarctation of the aorta beyond infancy: a 10–28 years follow-up with particular reference to late systemic hypertension. Am J Cardiol 51:1481–1488PubMedCrossRefGoogle Scholar
  6. de Frutos S, Caldwell E, Nitta CH, Kanagy NL, Wang J, Wang W, Walker MK, Gonzalez Bosc LV (2010) NFATc3 contributes to intermittent hypoxia-induced arterial remodeling in mice. Am J Physiol Heart Circ Physiol 299:H356–H363PubMedCentralPubMedGoogle Scholar
  7. Devlin RD, Du Z, Buccilli V, Jorgetti V, Canalis E (2002) Transgenic mice overexpressing insulin-like growth factor binding protein-5 display transiently decreased osteoblastic function and osteopenia. Endocrinology 143:3955–3962PubMedCrossRefGoogle Scholar
  8. Dietz JA, Johnson KL, Massingham LJ, Schaper J, Horlitz M, Cowan J, Bianchi DW (2011) Comparison of extraction techniques for amniotic fluid supernatant demonstrates improved yield of cell-free fetal RNA. Prenat Diagn 31:598–599PubMedCrossRefGoogle Scholar
  9. Elsheikh M, Dunger DB, Conway GS, Wass JA (2002) Turner’s syndrome in adulthood. Endocr Rev 23:120–140PubMedGoogle Scholar
  10. FitzSimmons J, Fantel A, Shepard TH (1994) Growth parameters in mid-trimester fetal Turner syndrome. Early Hum Dev 38:121–129PubMedCrossRefGoogle Scholar
  11. Giordano R, Forno D, Lanfranco F, Manieri C, Ghizzoni L, Ghigo E (2011) Metabolic and cardiovascular outcomes in a group of adult patients with Turner’s syndrome under hormonal replacement therapy. Eur J Endocrinol 164:819–826PubMedCrossRefGoogle Scholar
  12. Gobert M, Lafaille JJ (2012) Maternal–fetal immune tolerance, block by block. Cell 150:7–9PubMedCentralPubMedCrossRefGoogle Scholar
  13. Gravholt CH (2004) Epidemiological, endocrine, and metabolic features in Turner syndrome. Eur J Endocrinol 151:657–687PubMedCrossRefGoogle Scholar
  14. Gravholt CH, Juul S, Naeraa RW, Hansen J (1998) Morbidity in Turner syndrome. J Clin Epidemiol 51:147–158PubMedCrossRefGoogle Scholar
  15. Hall JG, Sybert VP, Williamson RA, Risher NL, Reed SD (1982) Turner’s syndrome. West J Med 137:32–44Google Scholar
  16. Hintz RL (2002) SHOX mutations. Rev Endocr Metab Disord 3:363–367PubMedCrossRefGoogle Scholar
  17. Horsley V, Pavlath GK (2002) NFAT: ubiquitous regulator of cell differentiation and adaptation. J Cell Biol 156:771–774PubMedCentralPubMedCrossRefGoogle Scholar
  18. Hui L, Slonim DK, Wick HC, Johnson KL, Bianchi DW (2012a) The amniotic fluid transcriptome: a source of novel information about human fetal development. Obstet Gynecol 119:111–118PubMedCentralPubMedCrossRefGoogle Scholar
  19. Hui L, Slonin DK, Wick HC, Johnson KL, Koide K, Bianchi DW (2012b) Novel neurodevelopmental information revealed in amniotic fluid supernatant transcripts from fetuses with trisomies 18 and 21. Hum Genet 131:1751–1759PubMedCentralPubMedCrossRefGoogle Scholar
  20. Jørgensen KT, Rostgaard K, Bache I, Biggar RJ, Nielsen NM, Tommerup N, Frisch M (2010) Autoimmune diseases in women with Turner’s syndrome. Arthr Rheum 62:658–666CrossRefGoogle Scholar
  21. Kanatani M, Sugimoto T, Nishiyama K, Chihara K (2000) Stimulatory effect of insulin-like growth factor binding protein-5 on mouse osteoclast formation and osteoclastic bone-resorbing activity. J Bone Miner Res 15:902–910PubMedCrossRefGoogle Scholar
  22. Kenny D, Polson JW, Martin RP, Paton JF, Wolf AR (2011) Hypertension and coarctation of the aorta: an inevitable consequence of developmental pathophysiology. Hypertens Res 34:543–547PubMedCrossRefGoogle Scholar
  23. Kim KS, Seu YB, Baek SH, Kim MJ, Kim KJ, Kim JH, Kim JR (2007) Induction of cellular senescence by insulin-like growth factor binding protein-5 through a p53-dependent mechanism. Mol Biol Cell 18:4543–4552PubMedCentralPubMedCrossRefGoogle Scholar
  24. Koide K, Slonim DK, Johnson KL, Tantravahi U, Cowan JM, Bianchi DW (2011) Transcriptomic analysis of cell-free fetal RNA suggests a specific molecular phenotype in trisomy 18. Hum Genet 129:295–305PubMedCentralPubMedCrossRefGoogle Scholar
  25. Kojima H, Kunimoto H, Inoue T, Nakajima K (2012) The STAT3–IGFBP5 axis is critical for IL-6/gp130-induced premature senescence in human fibroblasts. Cell Cycle 11:730–739PubMedCrossRefGoogle Scholar
  26. Larrabee PB, Johnson KL, Lai C, Ordovas J, Cowan JM, Tantravahi U, Bianchi DW (2005) Global gene expression analysis of the living human fetus using cell-free messenger RNA in amniotic fluid. JAMA 293:836–842PubMedCrossRefGoogle Scholar
  27. Nielsen J, Wohlert M (1991) Chromosome abnormalities found among 34,910 newborn children: results from a 13-year incidence study in Arhus, Denmark. Hum Genet 87:81–83PubMedCrossRefGoogle Scholar
  28. Papp C, Beke A, Mezi G, Szigeti Z, Ban Z, Papp Z (2006) Prenatal diagnosis of Turner syndrome; report on 69 cases. J Ultrasound Med 25:711–717PubMedGoogle Scholar
  29. Pavlidis P, Li Q, Noble WS (2003) The effect of replication on gene expression microarray experiments. Bioinformatics 19(13):1620–1627PubMedCrossRefGoogle Scholar
  30. Ross JL, Feuillan P, Long LM, Kowal K, Kushner H, Cutler GB Jr (1995) Lipid abnormalities in Turner syndrome. J Pediatr 126:242–245PubMedCrossRefGoogle Scholar
  31. Salih DA, Tripathi G, Holding C, Szestak TA, Gonzalez MI, Carter EJ, Cobb LJ, Eisemann JE, Pell JM (2004) Insulin-like growth factor-binding protein 5 (Igfbp5) compromises survival, growth, muscle development, and fertility in mice. Proc Natl Acad Sci USA 101:4314–4319PubMedCentralPubMedCrossRefGoogle Scholar
  32. 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 106:9425–9429PubMedCentralPubMedCrossRefGoogle Scholar
  33. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101:6062–6067PubMedCentralPubMedCrossRefGoogle Scholar
  34. Tyler C, Edman JC (2004) Down syndrome, Turner syndrome, and Klinefelter syndrome: primary care throughout the life span. Prim Care 31:627–648PubMedCrossRefGoogle Scholar
  35. Van PL, Bakalov VD, Bondy CA (2006) Monosomy for the X-chromosome is associated with an atherogenic lipid profile. J Clin Endocrinol Metab 91:2867–2870PubMedCrossRefGoogle Scholar
  36. Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW 3rd, Su AI (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 10:R130PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Lauren J. Massingham
    • 1
    Email author
  • Kirby L. Johnson
    • 2
  • Thomas M. Scholl
    • 3
  • Donna K. Slonim
    • 2
    • 4
  • Heather C. Wick
    • 4
  • Diana W. Bianchi
    • 1
  1. 1.Mother Infant Research Institute and Department of PediatricsFloating Hospital for Children at Tufts Medical CenterBostonUSA
  2. 2.Tufts University School of MedicineBostonUSA
  3. 3.Integrated Genetics, Esoterix Genetic LaboratoriesLLC, A Subsidiary of Laboratory Corporation of America® HoldingsWestboroughUSA
  4. 4.Department of Computer ScienceTufts UniversityMedfordUSA

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