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Jasinska AJ, Rostamian D, Davis AT, Kavanagh K. Transcriptomic Analysis of Cell-free Fetal RNA in the Amniotic Fluid of Vervet Monkeys ( Chlorocebus sabaeus). Comp Med 2020; 70:67-74. [PMID: 31969210 PMCID: PMC7024774 DOI: 10.30802/aalas-cm-19-000037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/22/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022]
Abstract
NHP are important translational models for understanding the genomic underpinnings of growth, development, fetal programming, and predisposition to disease, with potential for the development of early health biomarkers. Understanding how prenatal gene expression is linked to pre- and postnatal health and development requires methods for assessing the fetal transcriptome. Here we used RNAseq methodology to analyze the expression of cell-free fetal RNA in the amniotic fluid supernatant (AFS) of vervet monkeys. Despite the naturally high level of degradation of free-floating RNA, we detected more than 10,000 gene transcripts in vervet AFS. The most highly expressed genes were H19, IGF2, and TPT1, which are involved in embryonic growth and glycemic health. We noted global similarities in expression profiles between vervets and humans, with genes involved in embryonic growth and glycemic health among the genes most highly expressed in AFS. Our study demonstrates both the feasibility and usefulness of prenatal transcriptomic profiles, by using amniocentesis procedures to obtain AFS and cell-free fetal RNA from pregnant vervets.
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Affiliation(s)
- Anna J Jasinska
- Center for Neurobehavioral Genetics, University of California-Los Angeles, Los Angeles, California; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland;,
| | - Dalar Rostamian
- Center for Neurobehavioral Genetics, University of California-Los Angeles, Los Angeles, California
| | - Ashley T Davis
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Kylie Kavanagh
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina; Department of Biomedicine, University of Tasmania, Hobart, Australia
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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 (24.5±1.0 weeks); 10 archived amniotic fluid supernatant from sex and gestational age-matched euploid fetuses without myelomeningocele were used as controls (20.9±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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Hui L, Beard S, Hannan NJ. Measuring fetal brain and lung transcripts in amniotic fluid supernatant: a comparison of digital PCR and RT-qPCR methods. J Matern Fetal Neonatal Med 2017; 31:3191-3196. [PMID: 28805106 DOI: 10.1080/14767058.2017.1367378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
PURPOSE Amniotic fluid (AF) cell-free RNA is a promising source of information regarding fetal physiology. Digital PCR (dPCR) is a direct approach to nucleic acid detection that reports absolute transcript copy number. The aim of this study was to compare quantification of cell-free fetal brain and lung RNA transcripts in AF by reverse transcription-qPCR (RT-qPCR) and dPCR. MATERIAL AND METHODS Prospective hospital-based study was performed in 2016-2017. Pulmonary genes were quantified in term AF samples collected at elective cesarean birth; neurodevelopmental genes were measured in preterm samples (<34 weeks) obtained from women undergoing clinically-indicated amniocentesis. RESULTS All 11 women in the term cohort had three lung transcripts and a reference gene successfully amplified from their AF supernatant using RT-qPCR and dPCR. SFTPC was the most abundant lung transcript, present in higher concentrations than the reference gene in seven of the eleven samples. Neurodevelopmental gene transcripts in 12 preterm pregnancies were less reliably detected by both methods and were present in low copy numbers (<10 copies/μl). We observed significant positive correlations between transcript quantification by RT-qPCR and dPCR. CONCLUSION This study confirms the presence of several potential mRNA markers of lung and brain development with dPCR and RT-qPCR, and a high correlation between the two methods. Transcripts of presumed fetal brain origin are present in very low copy numbers, which presents challenges to their feasibility as biomarkers of neurodevelopment.
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Affiliation(s)
- Lisa Hui
- a Mercy Perinatal, Mercy Hospital for Women , Heidelberg , Australia.,b Department of Obstetrics and Gynecology, Translational Obstetrics Group , University of Melbourne , Heidelberg , Australia
| | - Sally Beard
- a Mercy Perinatal, Mercy Hospital for Women , Heidelberg , Australia.,b Department of Obstetrics and Gynecology, Translational Obstetrics Group , University of Melbourne , Heidelberg , Australia
| | - Natalie J Hannan
- a Mercy Perinatal, Mercy Hospital for Women , Heidelberg , Australia.,b Department of Obstetrics and Gynecology, Translational Obstetrics Group , University of Melbourne , Heidelberg , Australia
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Zwemer LM, Nolin SL, Okamoto PM, Eisenberg M, Wick HC, Bianchi DW. Global transcriptome dysregulation in second trimester fetuses with FMR1 expansions. Prenat Diagn 2016; 37:43-52. [PMID: 27646161 DOI: 10.1002/pd.4928] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/30/2016] [Accepted: 09/14/2016] [Indexed: 02/06/2023]
Abstract
OBJECTIVE We tested the hypothesis that FMR1 expansions would result in global gene dysregulation as early as the second trimester of human fetal development. METHOD Using cell-free fetal RNA obtained from amniotic fluid supernatant and expression microarrays, we compared RNA levels in samples from fetuses with premutation or full mutation allele expansions with control samples. RESULTS We found clear signals of differential gene expression relating to a variety of cellular functions, including ubiquitination, mitochondrial function, and neuronal/synaptic architecture. Additionally, among the genes showing differential gene expression, we saw links to related diseases of intellectual disability and motor function. Finally, within the unique molecular phenotypes established for each mutation set, we saw clear signatures of mitochondrial dysfunction and disrupted neurological function. Patterns of differential gene expression were very different in male and female fetuses with premutation alleles. CONCLUSION These results support a model for which genetic misregulation during fetal development may set the stage for late clinical manifestations of FMR1-related disorders. © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Lillian M Zwemer
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | - Sarah L Nolin
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Patricia M Okamoto
- Integrated Genetics/Laboratory Corporation of America® Holdings, Westborough, MA, USA
| | - Marcia Eisenberg
- Laboratory Corporation of America® Holdings, Research Triangle Park, NC, USA
| | - Heather C Wick
- Department of Computer Science, Tufts University, Medford, MA, USA
| | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
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Vora NL, Smeester L, Boggess K, Fry RC. Investigating the Role of Fetal Gene Expression in Preterm Birth. Reprod Sci 2016; 24:824-828. [PMID: 27678095 DOI: 10.1177/1933719116670038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Second-trimester amniotic fluid supernatant (AFS) contains cell-free fetal RNA (cffRNA) transcripts that can provide information about fetal gene expression. In a retrospective case-control study, we measured second-trimester fetal gene expression using cffRNA extracted from AFS in women who had spontaneous preterm birth (sPTB) <34 weeks and in women who delivered >37 weeks. We extracted cffRNA from AFS of women with singletons who had second-trimester genetic amniocenteses. Twenty-one gravidas who had sPTB and 21 term controls were matched 1:1 for maternal age, fetal sex, race, gestational age (GA) at the time of amniocentesis, and medication exposure. Cell-free fetal RNA was extracted and hybridized to a customized 65-gene NanoString panel containing genes related to oxidative stress, inflammation, and hypothalamic-pituitary-adrenal (HPA) axis and included 15 housekeeping genes. Two models were run, 1 examining sPTB in relation to case/control status and 1 examining sPTB in relation to GA as a continuous variable. Among cases, the gene expression of nitric oxide synthase 1 ( NOS1), d-aspartate oxidase ( DDO), and Beta-2-microglobulin ( B2M) was higher than controls ( P value < .05; false discovery rate-corrected Q value of ≤0.10). Nitric oxide synthase 1 and DDO are genes associated with oxidative stress; B2M is a marker of the fetal inflammatory response. Fetal HPA gene expression is not associated with GA at delivery or sPTB in second-trimester AFS. Alterations of fetal gene expression related to inflammation and oxidative stress antedate clinical symptoms and may be useful for early identification of patients at risk of having an sPTB.
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Affiliation(s)
- Neeta L Vora
- 1 Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynecology, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa Smeester
- 2 Department of Environmental Sciences and Engineering, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Kim Boggess
- 1 Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynecology, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C Fry
- 2 Department of Environmental Sciences and Engineering, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
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Hui L, Tong S, Kaitu'u-Lino TJ, Hannan NJ. A comparison of sample collection methods for quantifying cell-free fetal neurodevelopment transcripts in amniotic fluid. BMC Res Notes 2016; 9:335. [PMID: 27389196 PMCID: PMC4937574 DOI: 10.1186/s13104-016-2146-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023] Open
Abstract
Background Cell-free RNA (cfRNA) transcripts known to be expressed by the fetal brain are detectable by quantitative reverse transcription PCR (RT-qPCR) in amniotic fluid and represent potential biomarkers of neurodevelopment. The aim of this study was to compare the cfRNA yields from amniotic fluid (AF) collected in a commercial RNA stabilization product with the traditional method of freezing alone. Findings Thirteen women undergoing elective Cesarean birth at term without labor had whole AF collected at the time of uterine incision, prior to membrane rupture. Patient samples were split between Streck RNA blood collection tubes (BCT) and plain sterile polypropylene centrifuge tubes. Cell-free RNA from the AF supernatant was extracted according to a previously published protocol. RT qPCR was performed for the reference gene GAPDH, and three genes associated with neurodevelopment (NRXN3, NTRK3, and ZBTB18). The yield from samples collected in Streck RNA BCT and plain centrifuge tubes were compared with the paired t test. GAPDH, NRXN3 and ZBTB18 amplified successfully in all samples, but NTRK3 did not. The RNA yield was significantly lower in samples collected in the Streck RNA BCT compared with the traditional storage method of freezing alone for all three successfully amplified genes (p < 0.0001). Conclusions Selected cfRNA neurodevelopment transcripts are consistently detectable in third trimester AF. There appears to be no benefit in collecting AF in Streck RNA BCT for quantitative studies of AF cell-free RNA.
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Affiliation(s)
- Lisa Hui
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Rd, Heidelberg, VIC, 3084, Australia. .,Public Health Genetics, Murdoch Childrens Research Institute, Parkville, VIC, Australia.
| | - Stephen Tong
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Rd, Heidelberg, VIC, 3084, Australia
| | - Tu'Uhevaha J Kaitu'u-Lino
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Rd, Heidelberg, VIC, 3084, Australia
| | - Natalie J Hannan
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Rd, Heidelberg, VIC, 3084, Australia
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Kamath-Rayne BD, Du Y, Hughes M, Wagner EA, Muglia LJ, DeFranco EA, Whitsett JA, Salomonis N, Xu Y. Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity. BMC Med Genomics 2015; 8:67. [PMID: 26493725 PMCID: PMC4619218 DOI: 10.1186/s12920-015-0138-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/23/2015] [Indexed: 02/03/2023] Open
Abstract
Background Amniotic fluid (AF) is a proximal fluid to the fetus containing higher amounts of cell-free fetal RNA/DNA than maternal serum, thereby making it a promising source for identifying novel biomarkers that predict fetal development and organ maturation. Our aim was to compare AF transcriptomic profiles at different time points in pregnancy to demonstrate unique genetic signatures that would serve as potential biomarkers indicative of fetal maturation. Methods We isolated AF RNA from 16 women at different time points in pregnancy: 4 from 18 to 24 weeks, 6 from 34 to 36 weeks, and 6 from 39 to 40 weeks. RNA-sequencing was performed on cell-free RNA. Gene expression and splicing analyses were performed in conjunction with cell-type and pathway predictions. Results Sample-level analysis at different time points in pregnancy demonstrated a strong correlation with cell types found in the intrauterine environment and fetal respiratory, digestive and external barrier tissues of the fetus, using high-confidence cellular molecular markers. While some RNAs and splice variants were present throughout pregnancy, many transcripts were uniquely expressed at different time points in pregnancy and associated with distinct neonatal co-morbidities (respiratory distress and gavage feeding), indicating fetal immaturity. Conclusion The AF transcriptome exhibits unique cell/organ-selective expression patterns at different time points in pregnancy that can potentially identify fetal organ maturity and predict neonatal morbidity. Developing novel biomarkers indicative of the maturation of multiple organ systems can improve upon our current methods of fetal maturity testing which focus solely on the lung, and will better inform obstetrical decisions regarding delivery timing. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0138-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Beena D Kamath-Rayne
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - Yina Du
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - Maria Hughes
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - Erin A Wagner
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - Louis J Muglia
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - Emily A DeFranco
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Maternal-Fetal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Jeffrey A Whitsett
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - Nathan Salomonis
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - Yan Xu
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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Massingham LJ, Johnson KL, Scholl TM, Slonim DK, Wick HC, Bianchi DW. Amniotic fluid RNA gene expression profiling provides insights into the phenotype of Turner syndrome. Hum Genet 2014; 133:1075-82. [PMID: 24850140 PMCID: PMC4384642 DOI: 10.1007/s00439-014-1448-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 05/13/2014] [Indexed: 12/24/2022]
Abstract
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.
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Affiliation(s)
- Lauren J. Massingham
- Mother Infant Research Institute and Department of Pediatrics, Floating Hospital for Children at Tufts Medical Center, Boston, Massachusetts
| | | | - Thomas M. Scholl
- Integrated Genetics, Esoterix Genetic Laboratories, LLC, a subsidiary of Laboratory Corporation of America® Holdings, Westborough, MA
| | - Donna K. Slonim
- Tufts University School of Medicine, Boston, MA
- Dept. of Computer Science, Tufts University, Medford MA
| | | | - Diana W. Bianchi
- Mother Infant Research Institute and Department of Pediatrics, Floating Hospital for Children at Tufts Medical Center, Boston, Massachusetts
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Zwemer LM, Hui L, Wick HC, Bianchi DW. RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome. Prenat Diagn 2014; 34:1006-14. [PMID: 24852236 DOI: 10.1002/pd.4417] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/09/2014] [Accepted: 05/19/2014] [Indexed: 12/21/2022]
Abstract
OBJECTIVE The aim of this study was to compare the complexity of the amniotic fluid supernatant cell-free fetal transcriptome as described by RNA Sequencing (RNA-Seq) and gene expression microarrays. METHODS Cell-free fetal RNA from the amniotic fluid supernatant of five euploid mid-trimester samples was divided and prepared in tandem for analysis by either the Affymetrix HG-U133 Plus 2.0 Gene Chip microarray or Illumina HiSeq. Transcriptomes were assembled and compared on the basis of the presence of signal, rank-order gene expression, and pathway enrichment using Ingenuity Pathway Analysis (IPA). RNA-Seq data were also examined for evidence of alternative splicing. RESULTS Within individual samples, gene expression was strongly correlated (R = 0.43-0.57). Fewer expressed genes were observed using RNA-Seq than gene expression microarrays (4158 vs 8842). Most of the top pathways in the 'Physiological Systems Development and Function' IPA category were shared between platforms, although RNA-Seq yielded more significant p-values. Using RNA-Seq, examples of known alternative splicing were detected in several genes including H19 and IGF2. CONCLUSIONS In this pilot study, we found that expression microarrays gave a broader view of overall gene expression, while RNA-Seq demonstrated alternative splicing and specific pathways relevant to the developing fetus. The degraded nature of cell-free fetal RNA presented technical challenges for the RNA-Seq approach.
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Affiliation(s)
- Lillian M Zwemer
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
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Maternal obesity affects fetal neurodevelopmental and metabolic gene expression: a pilot study. PLoS One 2014; 9:e88661. [PMID: 24558408 PMCID: PMC3928248 DOI: 10.1371/journal.pone.0088661] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/11/2014] [Indexed: 11/19/2022] Open
Abstract
Objective One in three pregnant women in the United States is obese. Their offspring are at increased risk for neurodevelopmental and metabolic morbidity. Underlying molecular mechanisms are poorly understood. We performed a global gene expression analysis of mid-trimester amniotic fluid cell-free fetal RNA in obese versus lean pregnant women. Methods This prospective pilot study included eight obese (BMI≥30) and eight lean (BMI<25) women undergoing clinically indicated mid-trimester genetic amniocentesis. Subjects were matched for gestational age and fetal sex. Fetuses with abnormal karyotype or structural anomalies were excluded. Cell-free fetal RNA was extracted from amniotic fluid and hybridized to whole genome expression arrays. Genes significantly differentially regulated in 8/8 obese-lean pairs were identified using paired t-tests with the Benjamini-Hochberg correction (false discovery rate of <0.05). Biological interpretation was performed with Ingenuity Pathway Analysis and the BioGPS gene expression atlas. Results In fetuses of obese pregnant women, 205 genes were significantly differentially regulated. Apolipoprotein D, a gene highly expressed in the central nervous system and integral to lipid regulation, was the most up-regulated gene (9-fold). Apoptotic cell death was significantly down-regulated, particularly within nervous system pathways involving the cerebral cortex. Activation of the transcriptional regulators estrogen receptor, FOS, and STAT3 was predicted in fetuses of obese women, suggesting a pro-estrogenic, pro-inflammatory milieu. Conclusion Maternal obesity affects fetal neurodevelopmental and metabolic gene expression as early as the second trimester. These findings may have implications for postnatal neurodevelopmental and metabolic abnormalities described in the offspring of obese women.
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Abstract
OBJECTIVE To identify the tissue expression patterns and biological pathways enriched in term amniotic fluid cell-free fetal RNA by comparing functional genomic analyses of term and second-trimester amniotic fluid supernatants. METHODS This was a prospective whole genome microarray study comparing eight amniotic fluid samples collected from women at term who underwent prelabor cesarean delivery and eight second-trimester amniotic fluid samples from routine amniocenteses. A functional annotation tool was used to compare tissue expression patterns in term and second-trimester samples. Pathways analysis software identified physiologic systems, molecular and cellular functions, and upstream regulators that were significantly overrepresented in term amniotic fluid. RESULTS There were 2,871 significantly differentially regulated genes. In term amniotic fluid, tissue expression analysis showed enrichment of salivary gland, tracheal, and renal transcripts as compared with brain and embryonic neural cells in the second trimester. Functional analysis of genes upregulated at term revealed pathways that were highly specific for postnatal adaptation such as immune function, digestion, respiration, carbohydrate metabolism, and adipogenesis. Inflammation and prostaglandin synthesis, two key processes involved in normal labor, were also activated in term amniotic fluid. CONCLUSIONS Transcriptomic analysis of amniotic fluid cell-free fetal RNA detects fetal maturation processes activated in term pregnancy. These findings further develop the concept of amniotic fluid supernatant as a real-time gene expression "summary fluid" and support its potential for future studies of fetal development.
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Hui L, Wick HC, Moise KJ, Johnson A, Luks F, Haeri S, Johnson KL, Bianchi DW. Global gene expression analysis of amniotic fluid cell-free RNA from recipient twins with twin-twin transfusion syndrome. Prenat Diagn 2013; 33:873-83. [PMID: 23640821 DOI: 10.1002/pd.4150] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The objective of this study was to understand the biological pathways involved in twin-twin transfusion syndrome (TTTS) by performing global gene expression analysis of amniotic fluid (AF) cell-free RNA. METHODS A prospective whole transcriptome microarray study analyzing cell-free RNA in AF from TTTS recipient twins and singleton controls was carried out. Significantly differentially regulated genes in TTTS cases (N = 8) versus matched controls (N = 8) were identified and pathways analyses performed. Significant gene expression differences between stage II TTTS recipients (N = 5) and stage III TTTS recipients with abnormal Doppler measurements (N = 5) were also analyzed. RESULTS Analysis of paired data from TTTS cases and controls revealed differential expression of 801 genes, which were significantly enriched for neurological disease and cardiovascular system pathways. We also identified cardiovascular genes and pathways associated with the presence of critically abnormal Doppler measurements in stage III TTTS recipients. CONCLUSIONS This study provides the first transcriptome-wide data on the impact of TTTS on fetal development. Our results show that gene expression involving neurological and cardiovascular pathways are altered in recipient fetuses prior to surgical treatment. This has relevance for the origins of long-term complications seen in survivors and for the development of future fetal biomarkers.
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Affiliation(s)
- Lisa Hui
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA.
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