1
|
White M, Arif-Pardy J, Connor KL. Identification of novel nutrient-sensitive gene regulatory networks in amniocytes from fetuses with spina bifida. Reprod Toxicol 2023; 116:108333. [PMID: 36584796 DOI: 10.1016/j.reprotox.2022.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/14/2022] [Accepted: 12/26/2022] [Indexed: 12/28/2022]
Abstract
Neural tube defects (NTDs) remain among the most common congenital anomalies. Contributing risk factors include genetics and nutrient deficiencies, however, a comprehensive assessment of nutrient-gene interactions in NTDs is lacking. We applied a nutrient-focused gene expression analysis pipeline to identify nutrient-sensitive gene regulatory networks in amniocyte gene expression data (GSE4182) from fetuses with NTDs (cases; n = 3) and fetuses with no congenital anomalies (controls; n = 5). Differentially expressed genes (DEGs) were screened for having nutrient cofactors. Nutrient-dependent transcriptional regulators (TRs) that regulated DEGs, and nutrient-sensitive miRNAs with a previous link to NTDs, were identified. Of the 880 DEGs in cases, 10% had at least one nutrient cofactor. DEG regulatory network analysis revealed that 39% and 52% of DEGs in cases were regulated by 22 nutrient-sensitive miRNAs and 10 nutrient-dependent TRs, respectively. Zinc- and B vitamin-dependent gene regulatory networks (Zinc: 10 TRs targeting 50.6% of DEGs; B vitamins: 4 TRs targeting 37.7% of DEGs, 9 miRNAs targeting 17.6% of DEGs) were dysregulated in cases. We identified novel, nutrient-sensitive gene regulatory networks not previously linked to NTDs, which may indicate new targets to explore for NTD prevention or to optimise fetal development.
Collapse
Affiliation(s)
- Marina White
- Health Sciences, Carleton University, 1125 Colonel By Dr, Ottawa K1S 5B6, ON, Canada
| | - Jayden Arif-Pardy
- Health Sciences, Carleton University, 1125 Colonel By Dr, Ottawa K1S 5B6, ON, Canada
| | - Kristin L Connor
- Health Sciences, Carleton University, 1125 Colonel By Dr, Ottawa K1S 5B6, ON, Canada.
| |
Collapse
|
2
|
Liu P, Vossaert L. Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing. Prenat Diagn 2022; 42:686-696. [PMID: 35416301 PMCID: PMC10014115 DOI: 10.1002/pd.6146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/10/2022]
Abstract
DNA sequencing technologies for clinical genetic testing have been rapidly evolving in recent years, and steadily become more important within the field of prenatal diagnostics. This review aims to give an overview of recent developments and to describe how they have the potential to fill the gaps of the currently clinically implemented methods for prenatal diagnosis of various genetic disorders. It has been shown for postnatal testing that whole genome sequencing provides a set of added benefits compared to exome sequencing, and it is to be expected that this will be the case for prenatal testing as well. RNA-sequencing, already used postnatally, can provide valuable complementary data to DNA-based testing, and aid in variant interpretation. While not ready for clinical implementation, emerging technologies such as long-read and Hi-C sequencing analyses might add to the toolbox for interpreting the expanding genetic data sets generated by genome-wide sequencing. Lastly, we also discuss some more practical implications of introducing these emerging technologies, which generate larger and larger genomic data sets, in the prenatal field.
Collapse
Affiliation(s)
- Pengfei Liu
- Baylor College of Medicine and Baylor Genetics, Houston, Texas, USA
| | | |
Collapse
|
3
|
Kim MA, Lee EJ, Yang W, Shin HY, Kim YH, Kim JH. Identification of a novel gene signature in second-trimester amniotic fluid for the prediction of preterm birth. Sci Rep 2022; 12:3085. [PMID: 35361790 PMCID: PMC8971495 DOI: 10.1038/s41598-021-04709-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/30/2021] [Indexed: 11/09/2022] Open
Abstract
Preterm birth affects approximately 5% to 7% of live births worldwide and is the leading cause of neonatal morbidity and mortality. Amniotic fluid supernatant (AFS) contains abundant cell-free nucleic acids (cfNAs) that can provide genetic information associated with pregnancy complications. In the current study, cfNAs of AFS in the early second-trimester before the onset of symptoms of preterm birth were analyzed, and we compared gene expression levels between spontaneous preterm birth (n = 5) and term birth (n = 5) groups using sequencing analysis. Differential expression analyses detected 24 genes with increased and 6 genes with decreased expression in the preterm birth group compared to term birth. Upregulated expressions of RDH14, ZNF572, VOPP1, SERPINA12, and TCF15 were validated in an extended AFS sample by quantitative PCR (preterm birth group, n = 21; term birth group, n = 40). Five candidate genes displayed a significant increase in mRNA expression in immortalized trophoblast HTR-8/SVneo cell with H2O2 treatment. Moreover, the expression of five candidate genes was increased to more than twofold by pretreatment with lipopolysaccharide in HTR-8/SVneo cells. Changes in gene expression between preterm birth and term birth is strongly correlated with oxidative stress and infection during pregnancy. Specific expression patterns of genes could be used as potential markers for the early identification of women at risk of having a spontaneous preterm birth.
Collapse
Affiliation(s)
- Min-A Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Eun-Ju Lee
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Wookyeom Yang
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Ha-Yeon Shin
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Young-Han Kim
- Department of Obstetrics and Gynecology, Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Jae-Hoon Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
4
|
Abstract
Brain asymmetry is a hallmark of the human brain. Recent studies report a certain degree of abnormal asymmetry of brain lateralization between left and right brain hemispheres can be associated with many neuropsychiatric conditions. In this regard, some questions need answers. First, the accelerated brain asymmetry is programmed during the pre-natal period that can be called “accelerated brain decline clock”. Second, can we find the right biomarkers to predict these changes? Moreover, can we establish the dynamics of these changes in order to identify the right time window for proper interventions that can reverse or limit the neurological decline? To find answers to these questions, we performed a systematic online search for the last 10 years in databases using keywords. Conclusion: we need to establish the right in vitro model that meets human conditions as much as possible. New biomarkers are necessary to establish the “good” or the “bad” borders of brain asymmetry at the epigenetic and functional level as early as possible.
Collapse
|
5
|
Chou FS, Newton K, Wang PS. Quantifying Fetal Reprogramming for Biomarker Development in the Era of High-Throughput Sequencing. Genes (Basel) 2021; 12:genes12030329. [PMID: 33668810 PMCID: PMC7996299 DOI: 10.3390/genes12030329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022] Open
Abstract
Gestational hypertensive disorders continue to threaten the well-being of pregnant women and their offspring. The only current definitive treatment for gestational hypertensive disorders is delivery of the fetus. The optimal timing of delivery remains controversial. Currently, the available clinical tools do not allow for assessment of fetal stress in its early stages. Placental insufficiency and fetal growth restriction secondary to gestational hypertensive disorders have been shown to have long-term impacts on offspring health even into their adulthood, becoming one of the major focuses of research in the field of developmental origins of health and disease. Fetal reprogramming was introduced to describe the long-lasting effects of the toxic intrauterine environment on the growing fetus. With the advent of high-throughput sequencing, there have been major advances in research attempting to quantify fetal reprogramming. Moreover, genes that are found to be differentially expressed as a result of fetal reprogramming show promise in the development of transcriptional biomarkers for clinical use in detecting fetal response to placental insufficiency. In this review, we will review key pathophysiology in the development of placental insufficiency, existing literature on high-throughput sequencing in the study of fetal reprogramming, and considerations regarding research design from our own experience.
Collapse
Affiliation(s)
- Fu-Sheng Chou
- Division of Neonatology, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA;
- Correspondence: ; Tel.: +1-909-558-7448; Fax: +1-909-558-0298
| | - Krystel Newton
- Division of Neonatology, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA;
| | - Pei-Shan Wang
- PXT Research & Data Analytics, LLC, Rancho Cucamonga, CA 91739, USA;
| |
Collapse
|
6
|
Chen YH, Grigelioniene G, Newton PT, Gullander J, Elfving M, Hammarsjö A, Batkovskyte D, Alsaif HS, Kurdi WIY, Abdulwahab F, Shanmugasundaram V, Devey L, Bacrot S, Brodszki J, Huber C, Hamel B, Gisselsson D, Papadogiannakis N, Jedrycha K, Gürtl-Lackner B, Chagin AS, Nishimura G, Aschenbrenner D, Alkuraya FS, Laurence A, Cormier-Daire V, Uhlig HH. Absence of GP130 cytokine receptor signaling causes extended Stüve-Wiedemann syndrome. J Exp Med 2020; 217:133568. [PMID: 31914175 PMCID: PMC7062520 DOI: 10.1084/jem.20191306] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/07/2019] [Accepted: 11/14/2019] [Indexed: 01/25/2023] Open
Abstract
The gene IL6ST encodes GP130, the common signal transducer of the IL-6 cytokine family consisting of 10 cytokines. Previous studies have identified cytokine-selective IL6ST defects that preserve LIF signaling. We describe three unrelated families with at least five affected individuals who presented with lethal Stüve-Wiedemann–like syndrome characterized by skeletal dysplasia and neonatal lung dysfunction with additional features such as congenital thrombocytopenia, eczematoid dermatitis, renal abnormalities, and defective acute-phase response. We identified essential loss-of-function variants in IL6ST (a homozygous nonsense variant and a homozygous intronic splice variant with exon skipping). Functional tests showed absent cellular responses to GP130-dependent cytokines including IL-6, IL-11, IL-27, oncostatin M (OSM), and leukemia inhibitory factor (LIF). Genetic reconstitution of GP130 by lentiviral transduction in patient-derived cells reversed the signaling defect. This study identifies a new genetic syndrome caused by the complete lack of signaling of a whole family of GP130-dependent cytokines in humans and highlights the importance of the LIF signaling pathway in pre- and perinatal development.
Collapse
Affiliation(s)
- Yin-Huai Chen
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Phillip T Newton
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Jacob Gullander
- University and Regional Laboratories Department of Clinical Genetics, Lund, Sweden
| | - Maria Elfving
- Department of Clinical Sciences, Pediatrics, Skåne University Hospital Lund, Lund University, Lund, Sweden
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Dominyka Batkovskyte
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Wesam I Y Kurdi
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | | | | | - Séverine Bacrot
- Department of Clinical Genetics, INSERM UMR 1163, Université Paris Descartes-Sorbonne Paris cité, Institut Imagine, Hôpital Necker Enfants Malades, Paris, France
| | - Jana Brodszki
- Department of Obstetrics and Gynecology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Celine Huber
- Department of Clinical Genetics, INSERM UMR 1163, Université Paris Descartes-Sorbonne Paris cité, Institut Imagine, Hôpital Necker Enfants Malades, Paris, France
| | - Ben Hamel
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Sweden
| | - Nikos Papadogiannakis
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Huddinge, Sweden
| | - Katarina Jedrycha
- Department of Clinical Sciences, Pediatrics, Skåne University Hospital Lund, Lund University, Lund, Sweden
| | - Barbara Gürtl-Lackner
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Sweden
| | - Andrei S Chagin
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Institute for Regenerative Medicine, Sechenov University, Moscow, Russian Federation
| | - Gen Nishimura
- Center for Intractable Diseases, Saitama University Hospital, Saitama, Japan
| | | | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Arian Laurence
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Valérie Cormier-Daire
- Department of Clinical Genetics, INSERM UMR 1163, Université Paris Descartes-Sorbonne Paris cité, Institut Imagine, Hôpital Necker Enfants Malades, Paris, France
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.,Department of Paediatrics, University of Oxford, Oxford, UK.,Oxford National Institute for Health Research Biomedical Research Centre, Oxford, UK
| |
Collapse
|
7
|
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 (n = 30) or at term gestation (n = 68) were included. Expression profiling at exon level resolution was performed using Human Transcriptome Arrays. Differential expression was based on moderated t-test adjusted p < 0.05 and fold change > 1.25; for differential splicing, a splicing index > 2 and adjusted p < 0.05 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 (R > 0.79, p < 0.001) 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 p < 0.05). 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.
Collapse
Affiliation(s)
- Adi L Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 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, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 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, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 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, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 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, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 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, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 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, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 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, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 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, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 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, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 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, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 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.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Lum F, Narang V, Hue S, Chen J, McGovern N, Rajarethinam R, Tan JJL, Amrun SN, Chan Y, Lee CYP, Chua T, Yee W, Yeo NKW, Tan T, Liu X, Haldenby S, Leo Y, Ginhoux F, Chan JKY, Hiscox J, Chong C, Ng LFP. Immunological observations and transcriptomic analysis of trimester-specific full-term placentas from three Zika virus-infected women. Clin Transl Immunology 2019; 8:e01082. [PMID: 31709049 PMCID: PMC6831931 DOI: 10.1002/cti2.1082] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVES Effects of Zika virus (ZIKV) infection on placental development during pregnancy are unclear. METHODS Full-term placentas from three women, each infected with ZIKV during specific pregnancy trimesters, were harvested for anatomic, immunologic and transcriptomic analysis. RESULTS In this study, each woman exhibited a unique immune response with raised IL-1RA, IP-10, EGF and RANTES expression and neutrophil numbers during the acute infection phase. Although ZIKV NS3 antigens co-localised to placental Hofbauer cells, the placentas showed no anatomic defects. Transcriptomic analysis of samples from the placentas revealed that infection during trimester 1 caused a disparate cellular response centred on differential eIF2 signalling, mitochondrial dysfunction and oxidative phosphorylation. Despite these, the babies were delivered without any congenital anomalies. CONCLUSION These findings should translate to improve clinical prenatal screening procedures for virus-infected pregnant patients.
Collapse
Affiliation(s)
- Fok‐Moon Lum
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
| | - Vipin Narang
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
| | - Susan Hue
- Institute of Molecular and Cell BiologyAgency for Science, Technology and ResearchSingaporeSingapore
- Department of PathologyNational University Health SystemSingaporeSingapore
| | - Jie Chen
- KK Women's and Children's HospitalSingaporeSingapore
| | - Naomi McGovern
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - Ravisankar Rajarethinam
- Institute of Molecular and Cell BiologyAgency for Science, Technology and ResearchSingaporeSingapore
| | - Jeslin JL Tan
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
| | - Siti Naqiah Amrun
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
| | - Yi‐Hao Chan
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
- NUS Graduate School for Integrative Sciences and EngineeringNational University of SingaporeSingaporeSingapore
| | - Cheryl YP Lee
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
- NUS Graduate School for Integrative Sciences and EngineeringNational University of SingaporeSingaporeSingapore
| | - Tze‐Kwang Chua
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
| | - Wearn‐Xin Yee
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
| | - Nicholas KW Yeo
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
| | - Thiam‐Chye Tan
- Department of O&GKK Women's and Children's HospitalSingaporeSingapore
| | - Xuan Liu
- Centre for Genomic ResearchInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
- NIHR Health Protection Research Unit in Emerging and Zoonotic InfectionsUniversity of LiverpoolLiverpoolUK
| | - Sam Haldenby
- Centre for Genomic ResearchInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Yee‐sin Leo
- Communicable Diseases CentreInstitute of Infectious Diseases and EpidemiologyTan Tock Seng HospitalSingaporeSingapore
- National Centre for Infectious DiseasesSingaporeSingapore
- Saw Swee Hock School of Public HealthNational University of SingaporeSingaporeSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
| | - Florent Ginhoux
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
| | - Jerry KY Chan
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
- Department of Reproductive MedicineKK Women's and Children's HospitalSingaporeSingapore
- KK Research CentreKK Women's and Children's HospitalSingaporeSingapore
- Cancer and Stem Cell ProgramDuke–NUS Medical SchoolSingaporeSingapore
| | - Julian Hiscox
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
- NIHR Health Protection Research Unit in Emerging and Zoonotic InfectionsUniversity of LiverpoolLiverpoolUK
- Institute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
| | - Chia‐Yin Chong
- Department of PaediatricsKK Women's and Children's HospitalSingaporeSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
- Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Graduate Medical SchoolDuke‐NUS Medical SchoolSingaporeSingapore
| | - Lisa FP Ng
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingaporeSingapore
- NIHR Health Protection Research Unit in Emerging and Zoonotic InfectionsUniversity of LiverpoolLiverpoolUK
- Institute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| |
Collapse
|
10
|
Cho HY, Cho Y, Shin YJ, Park J, Shim S, Jung Y, Shim S, Cha D. Functional analysis of cell-free RNA using mid-trimester amniotic fluid supernatant in pregnancy with the fetal growth restriction. Medicine (Baltimore) 2018; 97:e9572. [PMID: 29480850 PMCID: PMC5943846 DOI: 10.1097/md.0000000000009572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The prediction and monitoring of fetal growth restriction (FGR) fetuses has become with the use of ultrasound. However, these tools lack the fundamental evidence for the growth of fetus with FGR excluding pathogenic factors.Amniotic fluid samples were obtained from pregnant women for fetal karyotyping and genetic diagnosis at 16 to 19 weeks of gestation. For this study, 15 FGR and 9 control samples were selected, and cell-free fetal RNA was isolated from each supernatant of the amniotic fluid for microarray analysis.In this study, 411 genes were differentially expressed between the FGR and control group. Of these genes, 316 genes were up-regulated, while 95 genes were down-regulated. In terms of gene ontology, the up-regulated genes were highly related to metabolic process as well as protein synthesis, while the down-regulated genes were related to receptor activity and biological adhesion. In terms of tissue-specific expression, the up-regulated genes were involved in various organs while down-regulated genes were involved only in the brain. In terms of organ-specific expression, many genes were enriched for B-cell lymphoma, pancreas, eye, placenta, epithelium, skin, and muscle. In the functional significance of gene, low-density lipoprotein receptor-related protein 10 (LRP10) was significantly increased (6-fold) and insulin-like growth factor (IGF-2) was dramatically increased (17-fold) in the FGR cases.The results show that the important brain-related genes are predominantly down-regulated in the intrauterine growth restriction fetuses during the second trimester of pregnancy. This study also suggested possible genes related to fetal development such as B-cell lymphoma, LRP10, and IGF-2. To monitor the fetal development, further study may be needed to elucidate the role of the genes identified.
Collapse
Affiliation(s)
- Hee Young Cho
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam
| | - Yeonkyung Cho
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University
| | - Yun-Jeong Shin
- Genetic Laboratory, CHA Gangnam Medical Center, CHA University, Seoul, Korea
| | - Jieun Park
- Genetic Laboratory, CHA Gangnam Medical Center, CHA University, Seoul, Korea
| | - Sunghan Shim
- Genetic Laboratory, CHA Gangnam Medical Center, CHA University, Seoul, Korea
| | - Yongwook Jung
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University
| | - Sungshin Shim
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University
| | - Donghyun Cha
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University
- Genetic Laboratory, CHA Gangnam Medical Center, CHA University, Seoul, Korea
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Pathological Brain Detection by a Novel Image Feature—Fractional Fourier Entropy. ENTROPY 2015. [DOI: 10.3390/e17127877] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
14
|
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.
Collapse
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.
| |
Collapse
|