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Tarca AL, Romero R, Erez O, Gudicha DW, Than NG, Benshalom-Tirosh N, Pacora P, Hsu CD, Chaiworapongsa T, Hassan SS, Gomez-Lopez N. Maternal whole blood mRNA signatures identify women at risk of early preeclampsia: a longitudinal study. J Matern Fetal Neonatal Med 2021; 34:3463-3474. [PMID: 31900005 PMCID: PMC10544754 DOI: 10.1080/14767058.2019.1685964] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022]
Abstract
PURPOSE To determine whether previously established mRNA signatures are predictive of early preeclampsia when evaluated by maternal cellular transcriptome analysis in samples collected before clinical manifestation. MATERIALS AND METHODS We profiled gene expression at exon-level resolution in whole blood samples collected longitudinally from 49 women with normal pregnancy (controls) and 13 with early preeclampsia (delivery <34βweeks of gestation). After preprocessing and removal of gestational age-related trends in gene expression, data were converted into Z-scores based on the mean and standard deviation among controls for six gestational-age intervals. The average Z-scores of mRNAs in each previously established signature considered herein were compared between cases and controls at 9-11, 11-17, 17-22, 22-28, 28-32, and 32-34βweeks of gestation.Results: (1) Average expression of the 16-gene untargeted cellular mRNA signature was higher in women diagnosed with early preeclampsia at 32-34βweeks of gestation, yet more importantly, also prior to diagnosis at 28-32βweeks and 22-28βweeks of gestation, compared to controls (all, pβ<β.05). (2) A combination of four genes from this signature, including a long non-protein coding RNA [H19 imprinted maternally expressed transcript (H19)], fibronectin 1 (FN1), tubulin beta-6 class V (TUBB6), and formyl peptide receptor 3 (FPR3) had a sensitivity of 0.85 (0.55-0.98) and a specificity of 0.92 (0.8-0.98) for prediction of early preeclampsia at 22-28βweeks of gestation. (3) H19, FN1, and TUBB6 were increased in women with early preeclampsia as early as 11-17βweeks of gestation (all, pβ<β.05). (4) After diagnosis at 32-34βweeks, but also prior to diagnosis at 11-17βweeks, women destined to have early preeclampsia showed a coordinated increase in whole blood expression of several single-cell placental signatures, including the 20-gene signature of extravillous trophoblast (all, pβ<β.05). (5) A combination of three mRNAs from the extravillous trophoblast signature (MMP11, SLC6A2, and IL18BP) predicted early preeclampsia at 11-17βweeks of gestation with a sensitivity of 0.83 (0.52-0.98) and specificity of 0.94 (0.79-0.99). CONCLUSIONS Circulating early transcriptomic markers for preeclampsia can be found either by untargeted profiling of the cellular transcriptome or by focusing on placental cell-specific mRNAs. The untargeted cellular mRNA signature was consistently increased in early preeclampsia after 22βweeks of gestation, and individual mRNAs of this signature were significantly increased as early as 11-17βweeks of gestation. Several single-cell placental signatures predicted future development of the disease at 11-17βweeks and were also increased in women already diagnosed at 32-34βweeks of gestation.
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Affiliation(s)
- Adi L. Tarca
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Computer Science, Wayne State University College of Engineering, Detroit, Michigan, USA
| | - Roberto Romero
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
- Detroit Medical Center, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Florida International University, Miami, FL, USA
| | - Offer Erez
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Maternity Department βD,β Division of Obstetrics and Gynecology, Soroka University Medical Center, School of Medicine, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Dereje W. Gudicha
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
| | - Nandor Gabor Than
- Systems Biology of Reproduction Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- Maternity Private Department, Kutvolgyi Clinical Block, Semmelweis University, Budapest, Hungary
| | - Neta Benshalom-Tirosh
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Percy Pacora
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Chaur-Dong Hsu
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Sonia S. Hassan
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
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Wang JY, Danial M, Soleymanzadeh C, Kim B, Xia Y, Kim K, Tassone F, Hagerman RJ, Rivera SM. Cortical gyrification and its relationships with molecular measures and cognition in children with the FMR1 premutation. Sci Rep 2020; 10:16059. [PMID: 32994518 PMCID: PMC7525519 DOI: 10.1038/s41598-020-73040-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 09/10/2020] [Indexed: 11/18/2022] Open
Abstract
Neurobiological basis for cognitive development and psychiatric conditions remains unexplored in children with the FMR1 premutation (PM). Knock-in mouse models of PM revealed defects in embryonic cortical development that may affect cortical folding. Cortical-folding complexity quantified using local gyrification index (LGI) was examined in 61 children (age 8β12Β years, 19/14 male/female PM carriers, 15/13 male/female controls). Whole-brain vertex-wise analysis of LGI was performed for group comparisons and correlations with IQ. Individuals with aberrant gyrification in 68 cortical areas were identified using Z-scores of LGI (hyper: Zββ₯β2.58, hypo: Zββ€βββ2.58). Significant group-by-sex-by-age interaction in LGI was detected in right inferior temporal and fusiform cortices, which correlated negatively with CGG repeat length in the PM carriers. Sixteen PM boys (hyper/hypo: 7/9) and 10 PM girls (hyper/hypo: 2/5, 3 both) displayed aberrant LGI in 1β17 regions/person while 2 control boys (hyper/hypo: 0/2) and 2 control girls (hyper/hypo: 1/1) met the same criteria in only 1 region/person. LGI in the precuneus and cingulate cortices correlated positively with IQ scores in PM and control boys while negatively in PM girls and no significant correlation in control girls. These findings reveal aberrant gyrification, which may underlie cognitive performance in children with the PM.
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Affiliation(s)
- Jun Yi Wang
- Center for Mind and Brain, University of California-Davis, 267 Cousteau Place, Davis, CA, 95618, USA. .,MIND Institute, University of California-Davis Medical Center, Sacramento, CA, 95817, USA.
| | - Merna Danial
- Center for Mind and Brain, University of California-Davis, 267 Cousteau Place, Davis, CA, 95618, USA.,Department of Psychology, University of California-Davis, Davis, CA, 95616, USA
| | - Cyrus Soleymanzadeh
- Center for Mind and Brain, University of California-Davis, 267 Cousteau Place, Davis, CA, 95618, USA.,Department of Psychology, University of California-Davis, Davis, CA, 95616, USA
| | - Bella Kim
- Center for Mind and Brain, University of California-Davis, 267 Cousteau Place, Davis, CA, 95618, USA.,Department of Psychology, University of California-Davis, Davis, CA, 95616, USA
| | - Yiming Xia
- Center for Mind and Brain, University of California-Davis, 267 Cousteau Place, Davis, CA, 95618, USA.,Department of Psychology, University of California-Davis, Davis, CA, 95616, USA
| | - Kyoungmi Kim
- MIND Institute, University of California-Davis Medical Center, Sacramento, CA, 95817, USA.,Department of Public Health Sciences, School of Medicine, University of California-Davis, Sacramento, CA, 95817, USA
| | - Flora Tassone
- MIND Institute, University of California-Davis Medical Center, Sacramento, CA, 95817, USA.,Department of Biochemistry and Molecular Medicine, School of Medicine, University of California-Davis, Sacramento, CA, 95817, USA
| | - Randi J Hagerman
- MIND Institute, University of California-Davis Medical Center, Sacramento, CA, 95817, USA.,Department of Pediatrics, School of Medicine, University of California-Davis, Sacramento, CA, 95817, USA
| | - Susan M Rivera
- Center for Mind and Brain, University of California-Davis, 267 Cousteau Place, Davis, CA, 95618, USA.,MIND Institute, University of California-Davis Medical Center, Sacramento, CA, 95817, USA.,Department of Psychology, University of California-Davis, Davis, CA, 95616, USA
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Tarca AL, Romero R, Pique-Regi R, Pacora P, Done B, Kacerovsky M, Bhatti G, Jaiman S, Hassan SS, Hsu CD, Gomez-Lopez N. Amniotic fluid cell-free transcriptome: a glimpse into fetal development and placental cellular dynamics during normal pregnancy. BMC Med Genomics 2020; 13:25. [PMID: 32050959 PMCID: PMC7017452 DOI: 10.1186/s12920-020-0690-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Background The amniotic fluid (AF) cell-free transcriptome is modulated by physiologic and pathologic processes during pregnancy. AF gene expression changes with advancing gestation reflect fetal development and organ maturation; yet, defining normal expression and splicing patterns for biomarker discovery in obstetrics requires larger heterogeneous cohorts, evaluation of potential confounding factors, and novel analytical approaches. Methods Women with a normal pregnancy who had an AF sample collected during midtrimester (nβ=β30) or at term gestation (nβ=β68) were included. Expression profiling at exon level resolution was performed using Human Transcriptome Arrays. Differential expression was based on moderated t-test adjusted pβ<β0.05 and fold change >β1.25; for differential splicing, a splicing index >β2 and adjusted pβ<β0.05 were required. Functional profiling was used to interpret differentially expressed or spliced genes. The expression of tissue-specific and cell-type specific signatures defined by single-cell genomics was quantified and correlated with covariates. In-silico validation studies were performed using publicly available datasets. Results 1) 64,071 genes were detected in AF, with 11% of the coding and 6% of the non-coding genes being differentially expressed between midtrimester and term gestation. Expression changes were highly correlated with those previously reported (Rβ>β0.79, pβ<β0.001) and featured increased expression of genes specific to the trachea, salivary glands, and lung and decreased expression of genes specific to the cardiac myocytes, uterus, and fetal liver, among others. 2) Single-cell RNA-seq signatures of the cytotrophoblast, Hofbauer cells, erythrocytes, monocytes, T and B cells, among others, showed complex patterns of modulation with gestation (adjusted pβ<β0.05). 3) In 17% of the genes detected, we found differential splicing with advancing gestation in genes related to brain development processes and immunity pathways, including some that were missed based on differential expression analysis alone. Conclusions This represents the largest AF transcriptomics study in normal pregnancy, reporting for the first time that single-cell genomic signatures can be tracked in the AF and display complex patterns of expression during gestation. We also demonstrate a role for alternative splicing in tissue-identity acquisition, organ development, and immune processes. The results herein may have implications for the development of fetal testing to assess placental function and fetal organ maturity.
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Affiliation(s)
- Adi L Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, πΈπ’ππππ πΎππππππ¦ πβπππ£ππ National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA. .,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA. .,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA.
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, πΈπ’ππππ πΎππππππ¦ πβπππ£ππ National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA. .,Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA. .,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA. .,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA. .,Detroit Medical Center, Detroit, MI, USA. .,Department of Pathology, Hutzel Women's Hospital, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Roger Pique-Regi
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, πΈπ’ππππ πΎππππππ¦ πβπππ£ππ National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - Percy Pacora
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, πΈπ’ππππ πΎππππππ¦ πβπππ£ππ National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - Bogdan Done
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, πΈπ’ππππ πΎππππππ¦ πβπππ£ππ National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
| | - Marian Kacerovsky
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, πΈπ’ππππ πΎππππππ¦ πβπππ£ππ National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - Gaurav Bhatti
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, πΈπ’ππππ πΎππππππ¦ πβπππ£ππ National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sunil Jaiman
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, πΈπ’ππππ πΎππππππ¦ πβπππ£ππ National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Pathology, Hutzel Women's Hospital, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sonia S Hassan
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, πΈπ’ππππ πΎππππππ¦ πβπππ£ππ National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Chaur-Dong Hsu
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, πΈπ’ππππ πΎππππππ¦ πβπππ£ππ National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, πΈπ’ππππ πΎππππππ¦ πβπππ£ππ National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA. .,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA. .,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicin, Detroit, MI, USA.
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Tarui T, Kim A, Flake A, McClain L, Stratigis JD, Fried I, Newman R, Slonim DK, Bianchi DW. Amniotic fluid transcriptomics reflects novel disease mechanisms in fetuses with myelomeningocele. Am J Obstet Gynecol 2017; 217:587.e1-587.e10. [PMID: 28735706 DOI: 10.1016/j.ajog.2017.07.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Cell-free RNA in amniotic fluid supernatant reflects developmental changes in gene expression in the living fetus, which includes genes that are specific to the central nervous system. Although it has been previously shown that central nervous system-specific transcripts are present in amniotic fluid supernatant, it is not known whether changes in the amniotic fluid supernatant transcriptome reflect the specific pathophysiologic condition of fetal central nervous system disorders. In myelomeningocele, there is open communication between the central nervous system and amniotic fluid. OBJECTIVES The purpose of this study was to identify molecular pathophysiologic changes and novel disease mechanisms that are specific to myelomeningocele by the analysis of amniotic fluid supernatant cell-free RNA in fetuses with open myelomeningocele. STUDY DESIGN Amniotic fluid supernatant was collected from 10 pregnant women at the time of the open myelomeningocele repair in the second trimester (24.5Β±1.0 weeks); 10 archived amniotic fluid supernatant from sex and gestational age-matched euploid fetuses without myelomeningocele were used as controls (20.9Β±0.9 weeks). Differentially regulated gene expression patterns were analyzed with the use of human genome expression arrays. RESULTS Fetuses with myelomeningocele had 284 differentially regulated genes (176 up- and 108 down-regulated) in amniotic fluid supernatant. Known genes that were associated with myelomeningocele (PRICKLE2, GLI3, RAB23, HES1, FOLR1) and novel dysregulated genes were identified in association with neurodevelopment and neuronal regeneration (up-regulated, GAP43 and ZEB1) or axonal growth and guidance (down-regulated, ACAP1). Pathway analysis demonstrated a significant contribution of inflammation to disease and a broad influence of Wnt signaling pathways (Wnt1, Wnt5A, ITPR1). CONCLUSION Transcriptomic analyses of living fetuses with myelomeningocele with the use of amniotic fluid supernatant cell-free RNA demonstrated differential regulation of specific genes and molecular pathways relevant to this central nervous system disorder, which resulted in a new understanding of pathophysiologic changes. The data also suggested the importance of pathways that involve secondary disease, such as inflammation, in myelomeningocele. These newly identified pathways may lead to hypotheses that can test novel therapeutic targets as adjuncts to fetal surgical repair.
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Ghidini A, Bianchi DW. Prenatal testing for neuropsychiatric disorders. Prenat Diagn 2017; 37:3-5. [PMID: 28097708 DOI: 10.1002/pd.4998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 11/12/2022]
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