Maternal plasma RNA sequencing

Clinical Biochemistry

Volumn 48, Issue 15, 2015, Pages 942-947

  Oudejans, Cees B M ^a  

^a VU UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Maternal plasma; Pre eclampsia; RNA sequencing

Indexed keywords

BIOLOGICAL MARKER; DNA; RNA;

BIOINFORMATICS; DNA SEQUENCE; EARLY DIAGNOSIS; FEASIBILITY STUDY; FETUS MORTALITY; FIRST TRIMESTER PREGNANCY; HELLP SYNDROME; HUMAN; MATERNAL MORBIDITY; MATERNAL MORTALITY; MATERNAL PLASMA; MOLECULAR LIBRARY; NON INVASIVE MEASUREMENT; PLACENTA FUNCTION; PREDICTION; PREECLAMPSIA; PRENATAL SCREENING; PRIORITY JOURNAL; PROTEIN SYNTHESIS; REVIEW; RIBODEPLETION; RNA ANALYSIS; RNA PROCESSING; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; TRISOMY; TRISOMY 13; TRISOMY 18; TRISOMY 21; ADVERSE EFFECTS; BIOLOGY; BLOOD; CHEMISTRY; FEMALE; GENETIC SCREENING; GENOMICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR DIAGNOSIS; MOLECULAR GENETICS; PATHOPHYSIOLOGY; PLASMA; PRE-ECLAMPSIA; PREGNANCY; PRENATAL DIAGNOSIS; PROCEDURES; SEQUENCE ANALYSIS; TRENDS;

BIOMARKERS; COMPUTATIONAL BIOLOGY; FEMALE; GENETIC TESTING; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MOLECULAR SEQUENCE ANNOTATION; PLASMA; PRE-ECLAMPSIA; PREGNANCY; PRENATAL DIAGNOSIS; RNA; SEQUENCE ANALYSIS, RNA;

EID: 84942125295     PISSN: 00099120     EISSN: 18732933     Source Type: Journal    
DOI: 10.1016/j.clinbiochem.2015.03.004     Document Type: Review

References (52)

1. Chiu R.W., Akolekar R., Zheng Y.W., Leung T.Y., Sun H., Chan K.C., et al. Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ 2011, 342:c7401.
2. Chen E.Z., Chiu R.W., Sun H., Akolekar R., Chan K.C., Leung T.Y., et al. Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing. PLoS One 2011, 6:e21791.
3. Bianchi D.W., Parker R.L., Wentworth J., Madankumar R., Saffer C., Das A.F., et al. DNA sequencing versus standard prenatal aneuploidy screening. N Engl J Med 2014, 370:799-808.
4. Straver R., Sistermans E.A., Holstege H., Visser A., Oudejans C.B., Reinders M.J. WISECONDOR: detection of fetal aberrations from shallow sequencing maternal plasma based on a within-sample comparison scheme. Nucleic Acids Res 2014, 42:e31.
5. Lo Y.M., Chan K.C., Sun H., Chen E.Z., Jiang P., Lun F.M., et al. Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med 2010, 2:61ra91.
6. Yu S.C., Chan K.C., Zheng Y.W., Jiang P., Liao G.J., Sun H., et al. Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing. Proc Natl Acad Sci U S A 2014, 111:8583-8588.
7. Go A.T., van Vugt J.M., Oudejans C.B. Non-invasive aneuploidy detection using free fetal DNA and RNA in maternal plasma: recent progress and future possibilities. Hum Reprod Update 2011, 17:372-382.
8. Steegers E.A., von Dadelszen P., Duvekot J.J., Pijnenborg R. Pre-eclampsia. Lancet 2010, 376(9741):631-644.
9. Redman C.W., Sargent I.L. Latest advances in understanding preeclampsia. Science 2005, 308:1592-1594.
10. Oudejans C.B., van Dijk M. Placental gene expression and pre-eclampsia. Placenta 2008, 29(Suppl. A):S78-S82.
11. Oudejans C.B., van Dijk M., Oosterkamp M., Lachmeijer A., Blankenstein M.A. Genetics of preeclampsia: paradigm shifts. Hum Genet 2007, 120:607-612.
12. Khalil A., Cowans N.J., Spencer K., Goichman S., Meiri H., Harrington K. First-trimester markers for the prediction of pre-eclampsia in women with a-priori high risk. Ultrasound Obstet Gynecol 2010, 35:671-679.
13. Pang W.W., Tsui M.H., Sahota D., Leung T.Y., Lau T.K., Lo Y.M., et al. A strategy for identifying circulating placental RNA markers for fetal growth assessment. Prenat Diagn 2009, 29:495-504.
14. Tsui N.B., Jiang P., Wong Y.F., Leung T.Y., Chan K.C., Chiu R.W., et al. Maternal plasma RNA sequencing for genome-wide transcriptomic profiling and identification of pregnancy-associated transcripts. Clin Chem 2014, 60:954-962.
15. Koh W., Pan W., Gawad C., Fan H.C., Kerchner G.A., Wyss-Coray T., et al. Noninvasive in vivo monitoring of tissue-specific global gene expression in humans. Proc Natl Acad Sci U S A 2014, 111:7361-7366.
16. van Dijk M., Mulders J., Poutsma A., Könst A.A., Lachmeijer A.M., Dekker G.A., et al. Maternal segregation of the Dutch preeclampsia locus at 10q22 with a new member of the winged helix gene family. Nat Genet 2005, 37:514-519.
17. van Dijk M., Thulluru H.K., Mulders J., Michel O.J., Poutsma A., Windhorst S., et al. HELLP babies link a novel lincRNA to the trophoblast cell cycle. J Clin Invest 2012, 122:4003-4011.
18. Oudejans C.B., Michel O.J., Janssen R., Habets R., Poutsma A., Sistermans E.A., et al. Susceptibility allele-specific loss of miR-1324-mediated silencing of the INO80B chromatin-assembly complex gene in pre-eclampsia. Hum Mol Genet 2015, 24:118-127.
19. Wong B.C., Chiu R.W., Tsui N.B., Chan K.C., Chan L.W., Lau T.K., et al. Circulating placental RNA in maternal plasma is associated with a preponderance of 5' mRNA fragments: implications for noninvasive prenatal diagnosis and monitoring. Clin Chem 2005, 51:1786-1795.
20. Turchinovich A., Weiz L., Langheinz A., Burwinkel B. Characterization of extracellular circulating microRNA. Nucleic Acids Res 2011, 39:7223-7233.
21. Nolte-'t Hoen E.N., Buermans H.P., Waasdorp M., Stoorvogel W., Wauben M.H., 't Hoen P.A. Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucleic Acids Res 2012, 40:9272-9285.
22. Arroyo J.D., Chevillet J.R., Kroh E.M., Ruf I.K., Pritchard C.C., Gibson D.F., et al. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci U S A 2011, 108:5003-5008.
23. Kshirsagar S.K., Alam S.M., Jasti S., Hodes H., Nauser T., Gilliam M., et al. Immunomodulatory molecules are released from the first trimester and term placenta via exosomes. Placenta 2012, 33:982-990.
24. Huang X., Yuan T., Tschannen M., Sun Z., Jacob H., Du M., et al. Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics 2013, 14:319.
25. Crescitelli R., Lässer C., Szabó T.G., Kittel A., Eldh M., Dianzani I., et al. Distinct RNA profiles in subpopulations of extracellular vesicles: apoptotic bodies, microvesicles and exosomes. J Extracell Vesicles Sep. 12 2013, 2.
26. Etheridge A., Gomes C.P., Pereira R.W., Galas D., Wang K. The complexity, function and applications of RNA in circulation. Front Genet 2013, 4:115.
27. Williams Z., Ben-Dov I.Z., Elias R., Mihailovic A., Brown M., Rosenwaks Z., et al. Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. Proc Natl Acad Sci U S A 2013, 110:4255-4260.
28. Raposo G., Stoorvogel W. Extracellular vesicles: exosomes, microvesicles, and friends. J Cell Biol 2013, 200:373-383.
29. Record M. Intercellular communication by exosomes in placenta: a possible role in cell fusion?. Placenta 2014, 35:297-302.
30. van der Pol E., Coumans F.A., Grootemaat A.E., Gardiner C., Sargent I.L., Harrison P., et al. Particle size distribution of exosomes and microvesicles determined by transmission electron microscopy, flow cytometry, nanoparticle tracking analysis, and resistive pulse sensing. J Thromb Haemost 2014, 12:1182-1192.
31. Vargas A., Zhou S., Éthier-Chiasson M., Flipo D., Lafond J., Gilbert C., et al. Syncytin proteins incorporated in placenta exosomes are important for cell uptake and show variation in abundance in serum exosomes from patients with preeclampsia. FASEB J 2014, 28:3703-3719.
32. Salomon C., Torres M.J., Kobayashi M., Scholz-Romero K., Sobrevia L., Dobierzewska A., et al. A gestational profile of placental exosomes in maternal plasma and their effects on endothelial cell migration. PLoS One 2014, 9:e98667.
33. Chevillet J.R., Kang Q., Ruf I.K., Briggs H.A., Vojtech L.N., Hughes S.M., et al. Quantitative and stoichiometric analysis of the microRNA content of exosomes. Proc Natl Acad Sci U S A 2014, 111:14888-14893.
34. Koppers-Lalic D., Hackenberg M., Bijnsdorp I.V., van Eijndhoven M.A., Sadek P., Sie D., et al. Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes. Cell Reprogram 2014, 8:1649-1658.
35. Houseley J., LaCava J., Tollervey D. RNA-quality control by the exosome. Nat Rev Mol Cell Biol 2006, 7:529-539.
36. Parker R., Song H. The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 2004, 11:121-127.
37. Houseley J., Tollervey D. The many pathways of RNA degradation. Cell 2009, 136:763-776.
38. Del Prete M.J., Robles M.S., Guáo A., Martínez-A C., Izquierdo M., Garcia-Sanz J.A. Degradation of cellular mRNA is a general early apoptosis-induced event. FASEB J 2002, 16:2003-2005.
39. Li S., Tighe S.W., Nicolet C.M., Grove D., Levy S., Farmerie W., et al. Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nat Biotechnol 2014, 32:915-925.
40. Salimullah M., Sakai M., Plessy C., Carninci P. NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes. Cold Spring Harb Protoc 2011, (1). [:pdb.prot5559].
41. Plessy C., Bertin N., Takahashi H., Simone R., Salimullah M., Lassmann T., et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods 2010, 7:528-534.
42. Jiang L., Schlesinger F., Davis C.A., Zhang Y., Li R., Salit M., et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res 2011, 21:1543-1551.
43. Wu A.R., Neff N.F., Kalisky T., Dalerba P., Treutlein B., Rothenberg M.E., et al. Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods 2014, 11:41-46.
44. Mercer T.R., Clark M.B., Crawford J., Brunck M.E., Gerhardt D.J., Taft R.J., et al. Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nat Protoc 2014, 9:989-1009.
45. Rapaport F., Khanin R., Liang Y., Pirun M., Krek A., Zumbo P., et al. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol 2013, 14:R95.
46. Trapnell C., Roberts A., Goff L., Pertea G., Kim D., Kelley D.R., et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012, 7:562-578.
47. Trapnell C., Hendrickson D.G., Sauvageau M., Goff L., Rinn J.L., Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 2013, 31:46-53.
48. Steijger T., Abril J.F., Engström P.G., Kokocinski F., Consortium R.G.A.S.P., Abril J.F., et al. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 2013, 10:1177-1184.
49. Pertea M., Pertea G.M., Antonescu C.M., Chang T.C., Mendell J.T., Salzberg S.L. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol Feb. 18 2015, 10.1038/nbt.3122.
50. Zhao S., Zhang B. A comprehensive evaluation of ensembl, RefSeq and UCSC annotations in the context of RNA-seq read mapping and gene quantification. BMC Genomics 2015, 16:97.
51. Iyer M.K., Niknafs Y.S., Malik R., Singhal U., Sahu A., Hosono Y., et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 2015 Jan 19, [[Epub ahead of print] PubMed PMID: 25599403]. 10.1038/ng.3192.
52. Fan H.C., Fu G.K., Fodor S.P. Expression profiling. Combinatorial labeling of single cells for gene expression cytometry. Science 2015, 347:1258367.