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Circular RNA Sequencing of Maternal Platelets: A Novel Tool for the Identification of Pregnancy-Specific Biomarkers. / Oudejans, Cees; Manders, Vera; Visser, Allerdien; Keijser, Remco; Min, Naomi; Poutsma, Ankie; Mulders, Joyce; van den Berkmortel, Tarah; Wigman, Di-Jan; Blanken, Britt; Jongejan, Aldo; Pajkrt, Eva; de Boer, Marjon; Sistermans, Erik A.; Sie, Daoud; Best, Myron G.; Würdinger, Tom; Afink, Gijs.

In: Clinical chemistry, Vol. 67, No. 3, 01.03.2021, p. 508-517.

Research output: Contribution to journalArticleAcademicpeer-review

Harvard

Oudejans, C, Manders, V, Visser, A, Keijser, R, Min, N, Poutsma, A, Mulders, J, van den Berkmortel, T, Wigman, D-J, Blanken, B, Jongejan, A, Pajkrt, E, de Boer, M, Sistermans, EA, Sie, D, Best, MG, Würdinger, T & Afink, G 2021, 'Circular RNA Sequencing of Maternal Platelets: A Novel Tool for the Identification of Pregnancy-Specific Biomarkers', Clinical chemistry, vol. 67, no. 3, pp. 508-517. https://doi.org/10.1093/clinchem/hvaa249

APA

Oudejans, C., Manders, V., Visser, A., Keijser, R., Min, N., Poutsma, A., Mulders, J., van den Berkmortel, T., Wigman, D-J., Blanken, B., Jongejan, A., Pajkrt, E., de Boer, M., Sistermans, E. A., Sie, D., Best, M. G., Würdinger, T., & Afink, G. (2021). Circular RNA Sequencing of Maternal Platelets: A Novel Tool for the Identification of Pregnancy-Specific Biomarkers. Clinical chemistry, 67(3), 508-517. https://doi.org/10.1093/clinchem/hvaa249

Vancouver

Author

Oudejans, Cees ; Manders, Vera ; Visser, Allerdien ; Keijser, Remco ; Min, Naomi ; Poutsma, Ankie ; Mulders, Joyce ; van den Berkmortel, Tarah ; Wigman, Di-Jan ; Blanken, Britt ; Jongejan, Aldo ; Pajkrt, Eva ; de Boer, Marjon ; Sistermans, Erik A. ; Sie, Daoud ; Best, Myron G. ; Würdinger, Tom ; Afink, Gijs. / Circular RNA Sequencing of Maternal Platelets: A Novel Tool for the Identification of Pregnancy-Specific Biomarkers. In: Clinical chemistry. 2021 ; Vol. 67, No. 3. pp. 508-517.

BibTeX

@article{d4203ef1c58049ee90eec725e5439dc7,
title = "Circular RNA Sequencing of Maternal Platelets: A Novel Tool for the Identification of Pregnancy-Specific Biomarkers",
abstract = "BACKGROUND: In the first trimester of pregnancy, the maternal platelet is directly involved in a positive feedback mechanism that facilitates invasion of the extravillous trophoblast into the maternal spiral arteries. Dysfunctional trophoblast invasion with defective deep placentation is primordial in the etiology of the {"}great obstetrical syndromes.{"} METHODS: In this proof-of-concept study, using transcriptome analysis of circular RNA (circRNA) following RNA sequencing of maternal platelets, we tested whether pregnancy-specific circRNA markers could be identified in the first trimester of normal pregnancies. Differential transcript expression analysis of circRNAs, as predicted by Accurate CircRNA Finder Suite, CircRNA Identifier (version 2), and Known and Novel Isoform Explorer, was done using thromboSeq.R with variation of multiple settings. Test performance was checked for (a) de novo circRNA identification using the novel platelet-specific Plt-circR4 as a positive control, (b) complete segregation of groups (pregnant vs nonpregnant) after heat map-dendrogram clustering, (c) identification of pregnancy-specific circRNA markers at a false discovery rate (FDR) <0.05, and (d) confirmation of differentially expressed circRNA markers with an FDR <0.05 by an independent method, reverse transcription-quantitative PCR. RESULTS: Of the differentially expressed circRNAs with P values <0.05, 41 circRNAs were upregulated (logFC >2), and 52 circRNAs were downregulated (logFC less than -2) in first-trimester platelet RNA. Of these, nuclear receptor-interacting protein 1 circRNA covering exons 2 and 3 of the 5'-untranslated region was pregnancy specific with upregulation in first-trimester maternal platelets compared to nonpregnant controls. CONCLUSION: CircRNA sequencing of first-trimester maternal platelets permits the identification of novel pregnancy-specific RNA biomarkers. Future use could include the assessment of maternal and fetal well-being.",
keywords = "NRIP1, RNA sequencing, circRNA, first trimester, platelet, pregnancy",
author = "Cees Oudejans and Vera Manders and Allerdien Visser and Remco Keijser and Naomi Min and Ankie Poutsma and Joyce Mulders and {van den Berkmortel}, Tarah and Di-Jan Wigman and Britt Blanken and Aldo Jongejan and Eva Pajkrt and {de Boer}, Marjon and Sistermans, {Erik A.} and Daoud Sie and Best, {Myron G.} and Tom W{\"u}rdinger and Gijs Afink",
note = "Publisher Copyright: {\textcopyright} American Association for Clinical Chemistry 2020. All rights reserved. For permissions, please email: journals.permissions@oup.com. Copyright: This record is sourced from MEDLINE/PubMed, a database of the U.S. National Library of Medicine",
year = "2021",
month = mar,
day = "1",
doi = "10.1093/clinchem/hvaa249",
language = "English",
volume = "67",
pages = "508--517",
journal = "Clinical chemistry",
issn = "0009-9147",
publisher = "American Association for Clinical Chemistry Inc.",
number = "3",

}

RIS

TY - JOUR

T1 - Circular RNA Sequencing of Maternal Platelets: A Novel Tool for the Identification of Pregnancy-Specific Biomarkers

AU - Oudejans, Cees

AU - Manders, Vera

AU - Visser, Allerdien

AU - Keijser, Remco

AU - Min, Naomi

AU - Poutsma, Ankie

AU - Mulders, Joyce

AU - van den Berkmortel, Tarah

AU - Wigman, Di-Jan

AU - Blanken, Britt

AU - Jongejan, Aldo

AU - Pajkrt, Eva

AU - de Boer, Marjon

AU - Sistermans, Erik A.

AU - Sie, Daoud

AU - Best, Myron G.

AU - Würdinger, Tom

AU - Afink, Gijs

N1 - Publisher Copyright: © American Association for Clinical Chemistry 2020. All rights reserved. For permissions, please email: journals.permissions@oup.com. Copyright: This record is sourced from MEDLINE/PubMed, a database of the U.S. National Library of Medicine

PY - 2021/3/1

Y1 - 2021/3/1

N2 - BACKGROUND: In the first trimester of pregnancy, the maternal platelet is directly involved in a positive feedback mechanism that facilitates invasion of the extravillous trophoblast into the maternal spiral arteries. Dysfunctional trophoblast invasion with defective deep placentation is primordial in the etiology of the "great obstetrical syndromes." METHODS: In this proof-of-concept study, using transcriptome analysis of circular RNA (circRNA) following RNA sequencing of maternal platelets, we tested whether pregnancy-specific circRNA markers could be identified in the first trimester of normal pregnancies. Differential transcript expression analysis of circRNAs, as predicted by Accurate CircRNA Finder Suite, CircRNA Identifier (version 2), and Known and Novel Isoform Explorer, was done using thromboSeq.R with variation of multiple settings. Test performance was checked for (a) de novo circRNA identification using the novel platelet-specific Plt-circR4 as a positive control, (b) complete segregation of groups (pregnant vs nonpregnant) after heat map-dendrogram clustering, (c) identification of pregnancy-specific circRNA markers at a false discovery rate (FDR) <0.05, and (d) confirmation of differentially expressed circRNA markers with an FDR <0.05 by an independent method, reverse transcription-quantitative PCR. RESULTS: Of the differentially expressed circRNAs with P values <0.05, 41 circRNAs were upregulated (logFC >2), and 52 circRNAs were downregulated (logFC less than -2) in first-trimester platelet RNA. Of these, nuclear receptor-interacting protein 1 circRNA covering exons 2 and 3 of the 5'-untranslated region was pregnancy specific with upregulation in first-trimester maternal platelets compared to nonpregnant controls. CONCLUSION: CircRNA sequencing of first-trimester maternal platelets permits the identification of novel pregnancy-specific RNA biomarkers. Future use could include the assessment of maternal and fetal well-being.

AB - BACKGROUND: In the first trimester of pregnancy, the maternal platelet is directly involved in a positive feedback mechanism that facilitates invasion of the extravillous trophoblast into the maternal spiral arteries. Dysfunctional trophoblast invasion with defective deep placentation is primordial in the etiology of the "great obstetrical syndromes." METHODS: In this proof-of-concept study, using transcriptome analysis of circular RNA (circRNA) following RNA sequencing of maternal platelets, we tested whether pregnancy-specific circRNA markers could be identified in the first trimester of normal pregnancies. Differential transcript expression analysis of circRNAs, as predicted by Accurate CircRNA Finder Suite, CircRNA Identifier (version 2), and Known and Novel Isoform Explorer, was done using thromboSeq.R with variation of multiple settings. Test performance was checked for (a) de novo circRNA identification using the novel platelet-specific Plt-circR4 as a positive control, (b) complete segregation of groups (pregnant vs nonpregnant) after heat map-dendrogram clustering, (c) identification of pregnancy-specific circRNA markers at a false discovery rate (FDR) <0.05, and (d) confirmation of differentially expressed circRNA markers with an FDR <0.05 by an independent method, reverse transcription-quantitative PCR. RESULTS: Of the differentially expressed circRNAs with P values <0.05, 41 circRNAs were upregulated (logFC >2), and 52 circRNAs were downregulated (logFC less than -2) in first-trimester platelet RNA. Of these, nuclear receptor-interacting protein 1 circRNA covering exons 2 and 3 of the 5'-untranslated region was pregnancy specific with upregulation in first-trimester maternal platelets compared to nonpregnant controls. CONCLUSION: CircRNA sequencing of first-trimester maternal platelets permits the identification of novel pregnancy-specific RNA biomarkers. Future use could include the assessment of maternal and fetal well-being.

KW - NRIP1

KW - RNA sequencing

KW - circRNA

KW - first trimester

KW - platelet

KW - pregnancy

UR - http://www.scopus.com/inward/record.url?scp=85102657530&partnerID=8YFLogxK

U2 - 10.1093/clinchem/hvaa249

DO - 10.1093/clinchem/hvaa249

M3 - Article

C2 - 33257975

VL - 67

SP - 508

EP - 517

JO - Clinical chemistry

JF - Clinical chemistry

SN - 0009-9147

IS - 3

ER -

ID: 15085076