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Huri M, Strambi N, Finazzi M, Manciucca G, Catalano G, Seravalli V, Di Tommaso M. The role of family history of preterm delivery in the individual risk of spontaneous preterm delivery: a case-control study. Arch Gynecol Obstet 2024; 309:2515-2519. [PMID: 37466687 PMCID: PMC11147892 DOI: 10.1007/s00404-023-07144-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023]
Abstract
PURPOSE To investigate the role of family history of preterm delivery (PTD) in the individual risk of spontaneous preterm delivery. METHODS A retrospective case-control study was conducted on 354 patients who delivered between 2018 and 2020. 177 women who delivered preterm were matched with 177 controls who had full-term delivery. A questionnaire was administered to investigate the family history of PTD of both the patient and her partner. Cases and controls were matched for the anamnestic risk factors for PTD. RESULTS Seventeen of 173 women (9.8%) in the PTD group reported being born preterm, compared to five of 169 women (2.9%) in the control group (p = 0.01), with an odds ratio (OR) of 3.57 (95% confidence interval, CI 1.29-9.92). Women who delivered preterm also reported more frequently having a sibling who was born preterm (12.4% vs. 4.2%, p = 0.01), with an OR of 3.18 (95% CI 1.31-7.7). No association was found between the partner's family history of premature delivery and the patient's risk of preterm delivery in the present pregnancy. CONCLUSIONS Pregnant patients who were born prematurely or who have siblings born preterm have an increased risk of preterm delivery in their own pregnancies. Assessment of female personal and family history of PTD should be used to identify women at risk of having a PTD in the present pregnancy.
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Affiliation(s)
- Mor Huri
- Obstetrics and Gynecology Unit, Division of Obstetrics and Gynecology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Noemi Strambi
- Obstetrics and Gynecology Unit, Division of Obstetrics and Gynecology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Marta Finazzi
- Obstetrics and Gynecology Unit, Division of Obstetrics and Gynecology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Giulia Manciucca
- Obstetrics and Gynecology Unit, Division of Obstetrics and Gynecology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Giovanna Catalano
- Obstetrics and Gynecology Unit, Division of Obstetrics and Gynecology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Viola Seravalli
- Obstetrics and Gynecology Unit, Division of Obstetrics and Gynecology, Department of Health Sciences, University of Florence, Florence, Italy.
| | - Mariarosaria Di Tommaso
- Obstetrics and Gynecology Unit, Division of Obstetrics and Gynecology, Department of Health Sciences, University of Florence, Florence, Italy
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Ward VC, Hawken S, Chakraborty P, Darmstadt GL, Wilson K. Estimating Gestational Age and Prediction of Preterm Birth Using Metabolomics Biomarkers. Clin Perinatol 2024; 51:411-424. [PMID: 38705649 DOI: 10.1016/j.clp.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Preterm birth (PTB) is a leading cause of morbidity and mortality in children aged under 5 years globally, especially in low-resource settings. It remains a challenge in many low-income and middle-income countries to accurately measure the true burden of PTB due to limited availability of accurate measures of gestational age (GA), first trimester ultrasound dating being the gold standard. Metabolomics biomarkers are a promising area of research that could provide tools for both early identification of high-risk pregnancies and for the estimation of GA and preterm status of newborns postnatally.
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Affiliation(s)
- Victoria C Ward
- Department of Pediatrics, Stanford University School of Medicine, 291 Campus Drive Li Ka Shing Building, Stanford, CA 94305, USA
| | - Steven Hawken
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Centre for Practice Changing Research, 501 Smyth Road, Box 201-B, Ottawa, Ontario, Canada K1H 8L6; School of Epidemiology and Public Health, University of Ottawa, 600 Peter Morand Crescent, Ottawa, Ontario, Canada K1G 5Z3.
| | - Pranesh Chakraborty
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, 415 Smyth Road, Ottawa, Ontario K1H 8M8, Canada; Department of Pediatrics, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa Ontario, Canada K1H 8M5
| | - Gary L Darmstadt
- Prematurity Research Center, Department of Pediatrics, Stanford University School of Medicine, 453 Quarry Road, Palo Alto, CA 94304, USA
| | - Kumanan Wilson
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Centre for Practice Changing Research, 501 Smyth Road, Box 201-B, Ottawa, Ontario, Canada K1H 8L6; Department of Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5; Bruyère Research Institute, 85 Primrose Avenue, Ottawa, Ontario, Canada K2A2E5
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Juaiti M, Feng Y, Tang Y, Liang B, Zha L, Yu Z. Integrated bioinformatics analysis and experimental animal models identify a robust biomarker and its correlation with the immune microenvironment in pulmonary arterial hypertension. Heliyon 2024; 10:e29587. [PMID: 38660271 PMCID: PMC11040037 DOI: 10.1016/j.heliyon.2024.e29587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Background Pulmonary arterial hypertension (PAH) represents a substantial global risk to human health. This study aims to identify diagnostic biomarkers for PAH and assess their association with the immune microenvironment through the utilization of sophisticated bioinformatics techniques. Methods Based on two microarray datasets, differentially expressed genes (DEGs) were detected, and hub genes underwent a sequence of machine learning analyses. After pathways associated with PAH were assessed by gene enrichment analysis, the identified genes were validated using external datasets and confirmed in a monocrotaline (MCT)-induced rat model. In addition, three algorithms were employed to estimate the proportions of various immune cell types, and the link between hub genes and immune cells was substantiated. Results Using SVM, LASSO, and WGCNA, we identified seven hub genes, including (BPIFA1, HBA2, HBB, LOC441081, PI15, S100A9, and WIF1), of which only BPIFA1 remained stable in the external datasets and was validated in an MCT-induced rat model. Furthermore, the results of the functional enrichment analysis established a link between PAH and both metabolism and the immune system. Correlation assessment showed that BPIFA1 expression in the MCP-counter algorithm was negatively associated with various immune cell types, positively correlated with macrophages in the ssGSEA algorithm, and correlated with M1 and M2 macrophages in the CIBERSORT algorithm. Conclusion BPIFA1 serves as a modulator of PAH, with the potential to impact the immune microenvironment and disease progression, possibly through its regulatory influence on both M1 and M2 macrophages.
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Affiliation(s)
- Mukamengjiang Juaiti
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Yilu Feng
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Yiyang Tang
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Benhui Liang
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Lihuang Zha
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Zaixin Yu
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
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4
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Hans N, Klein N, Faschingbauer F, Schneider M, Mayr A. Boosting distributional copula regression. Biometrics 2023; 79:2298-2310. [PMID: 36165288 DOI: 10.1111/biom.13765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022]
Abstract
Capturing complex dependence structures between outcome variables (e.g., study endpoints) is of high relevance in contemporary biomedical data problems and medical research. Distributional copula regression provides a flexible tool to model the joint distribution of multiple outcome variables by disentangling the marginal response distributions and their dependence structure. In a regression setup, each parameter of the copula model, that is, the marginal distribution parameters and the copula dependence parameters, can be related to covariates via structured additive predictors. We propose a framework to fit distributional copula regression via model-based boosting, which is a modern estimation technique that incorporates useful features like an intrinsic variable selection mechanism, parameter shrinkage and the capability to fit regression models in high-dimensional data setting, that is, situations with more covariates than observations. Thus, model-based boosting does not only complement existing Bayesian and maximum-likelihood based estimation frameworks for this model class but rather enables unique intrinsic mechanisms that can be helpful in many applied problems. The performance of our boosting algorithm for copula regression models with continuous margins is evaluated in simulation studies that cover low- and high-dimensional data settings and situations with and without dependence between the responses. Moreover, distributional copula boosting is used to jointly analyze and predict the length and the weight of newborns conditional on sonographic measurements of the fetus before delivery together with other clinical variables.
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Affiliation(s)
- Nicolai Hans
- Chair of Statistics and Data Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nadja Klein
- Chair of Statistics and Data Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Faschingbauer
- Department of Obstetrics and Gynecology, University Hospital of Erlangen, Erlangen, Germany
| | - Michael Schneider
- Department of Obstetrics and Gynecology, University Hospital of Erlangen, Erlangen, Germany
| | - Andreas Mayr
- Department of Medical Biometrics, Informatics and Epidemiology, Faculty of Medicine, University of Bonn, Bonn, Germany
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Multi-Omics Analysis of Lung Tissue Demonstrates Changes to Lipid Metabolism during Allergic Sensitization in Mice. Metabolites 2023; 13:metabo13030406. [PMID: 36984845 PMCID: PMC10054742 DOI: 10.3390/metabo13030406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/12/2023] Open
Abstract
Allergy and asthma pathogenesis are associated with the dysregulation of metabolic pathways. To understand the effects of allergen sensitization on metabolic pathways, we conducted a multi-omics study using BALB/cJ mice sensitized to house dust mite (HDM) extract or saline. Lung tissue was used to perform untargeted metabolomics and transcriptomics while both lung tissue and plasma were used for targeted lipidomics. Following statistical comparisons, an integrated pathway analysis was conducted. Histopathological changes demonstrated an allergic response in HDM-sensitized mice. Untargeted metabolomics showed 391 lung tissue compounds were significantly different between HDM and control mice (adjusted p < 0.05); with most compounds mapping to glycerophospholipid and sphingolipid pathways. Several lung oxylipins, including 14-HDHA, 8-HETE, 15-HETE, 6-keto-PGF1α, and PGE2 were significantly elevated in HDM-sensitized mice (p < 0.05). Global gene expression analysis showed upregulated calcium channel, G protein–signaling, and mTORC1 signaling pathways. Genes related to oxylipin metabolism such as Cox, Cyp450s, and cPla2 trended upwards. Joint analysis of metabolomics and transcriptomics supported a role for glycerophospholipid and sphingolipid metabolism following HDM sensitization. Collectively, our multi-omics results linked decreased glycerophospholipid and sphingolipid compounds and increased oxylipins with allergic sensitization; concurrent upregulation of associated gene pathways supports a role for bioactive lipids in the pathogenesis of allergy and asthma.
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Zhang B, He J, Hu J, Chalise P, Koestler DC. Improving the accuracy and internal consistency of regression-based clustering of high-dimensional datasets. Stat Appl Genet Mol Biol 2023; 22:sagmb-2022-0031. [PMID: 37489035 PMCID: PMC10891458 DOI: 10.1515/sagmb-2022-0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 05/31/2023] [Indexed: 07/26/2023]
Abstract
Component-wise Sparse Mixture Regression (CSMR) is a recently proposed regression-based clustering method that shows promise in detecting heterogeneous relationships between molecular markers and a continuous phenotype of interest. However, CSMR can yield inconsistent results when applied to high-dimensional molecular data, which we hypothesize is in part due to inherent limitations associated with the feature selection method used in the CSMR algorithm. To assess this hypothesis, we explored whether substituting different regularized regression methods (i.e. Lasso, Elastic Net, Smoothly Clipped Absolute Deviation (SCAD), Minmax Convex Penalty (MCP), and Adaptive-Lasso) within the CSMR framework can improve the clustering accuracy and internal consistency (IC) of CSMR in high-dimensional settings. We calculated the true positive rate (TPR), true negative rate (TNR), IC and clustering accuracy of our proposed modifications, benchmarked against the existing CSMR algorithm, using an extensive set of simulation studies and real biological datasets. Our results demonstrated that substituting Adaptive-Lasso within the existing feature selection method used in CSMR led to significantly improved IC and clustering accuracy, with strong performance even in high-dimensional scenarios. In conclusion, our modifications of the CSMR method resulted in improved clustering performance and may thus serve as viable alternatives for the regression-based clustering of high-dimensional datasets.
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Affiliation(s)
- Bo Zhang
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jianghua He
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jinxiang Hu
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Prabhakar Chalise
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Devin C Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
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The amniotic fluid proteome predicts imminent preterm delivery in asymptomatic women with a short cervix. Sci Rep 2022; 12:11781. [PMID: 35821507 PMCID: PMC9276779 DOI: 10.1038/s41598-022-15392-3] [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: 10/14/2021] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
Preterm birth, the leading cause of perinatal morbidity and mortality, is associated with increased risk of short- and long-term adverse outcomes. For women identified as at risk for preterm birth attributable to a sonographic short cervix, the determination of imminent delivery is crucial for patient management. The current study aimed to identify amniotic fluid (AF) proteins that could predict imminent delivery in asymptomatic patients with a short cervix. This retrospective cohort study included women enrolled between May 2002 and September 2015 who were diagnosed with a sonographic short cervix (< 25 mm) at 16–32 weeks of gestation. Amniocenteses were performed to exclude intra-amniotic infection; none of the women included had clinical signs of infection or labor at the time of amniocentesis. An aptamer-based multiplex platform was used to profile 1310 AF proteins, and the differential protein abundance between women who delivered within two weeks from amniocentesis, and those who did not, was determined. The analysis included adjustment for quantitative cervical length and control of the false-positive rate at 10%. The area under the receiver operating characteristic curve was calculated to determine whether protein abundance in combination with cervical length improved the prediction of imminent preterm delivery as compared to cervical length alone. Of the 1,310 proteins profiled in AF, 17 were differentially abundant in women destined to deliver within two weeks of amniocentesis independently of the cervical length (adjusted p-value < 0.10). The decreased abundance of SNAP25 and the increased abundance of GPI, PTPN11, OLR1, ENO1, GAPDH, CHI3L1, RETN, CSF3, LCN2, CXCL1, CXCL8, PGLYRP1, LDHB, IL6, MMP8, and PRTN3 were associated with an increased risk of imminent delivery (odds ratio > 1.5 for each). The sensitivity at a 10% false-positive rate for the prediction of imminent delivery by a quantitative cervical length alone was 38%, yet it increased to 79% when combined with the abundance of four AF proteins (CXCL8, SNAP25, PTPN11, and MMP8). Neutrophil-mediated immunity, neutrophil activation, granulocyte activation, myeloid leukocyte activation, and myeloid leukocyte-mediated immunity were biological processes impacted by protein dysregulation in women destined to deliver within two weeks of diagnosis. The combination of AF protein abundance and quantitative cervical length improves prediction of the timing of delivery compared to cervical length alone, among women with a sonographic short cervix.
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8
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Chakraborty D, Sharma N, Kour S, Sodhi SS, Gupta MK, Lee SJ, Son YO. Applications of Omics Technology for Livestock Selection and Improvement. Front Genet 2022; 13:774113. [PMID: 35719396 PMCID: PMC9204716 DOI: 10.3389/fgene.2022.774113] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 05/16/2022] [Indexed: 12/16/2022] Open
Abstract
Conventional animal selection and breeding methods were based on the phenotypic performance of the animals. These methods have limitations, particularly for sex-limited traits and traits expressed later in the life cycle (e.g., carcass traits). Consequently, the genetic gain has been slow with high generation intervals. With the advent of high-throughput omics techniques and the availability of multi-omics technologies and sophisticated analytic packages, several promising tools and methods have been developed to estimate the actual genetic potential of the animals. It has now become possible to collect and access large and complex datasets comprising different genomics, transcriptomics, proteomics, metabolomics, and phonemics data as well as animal-level data (such as longevity, behavior, adaptation, etc.,), which provides new opportunities to better understand the mechanisms regulating animals’ actual performance. The cost of omics technology and expertise of several fields like biology, bioinformatics, statistics, and computational biology make these technology impediments to its use in some cases. The population size and accurate phenotypic data recordings are other significant constraints for appropriate selection and breeding strategies. Nevertheless, omics technologies can estimate more accurate breeding values (BVs) and increase the genetic gain by assisting the section of genetically superior, disease-free animals at an early stage of life for enhancing animal productivity and profitability. This manuscript provides an overview of various omics technologies and their limitations for animal genetic selection and breeding decisions.
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Affiliation(s)
- Dibyendu Chakraborty
- Division of Animal Genetics and Breeding, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Ranbir Singh Pura, India
| | - Neelesh Sharma
- Division of Veterinary Medicine, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Ranbir Singh Pura, India
- *Correspondence: Neelesh Sharma, ; Young Ok Son,
| | - Savleen Kour
- Division of Veterinary Medicine, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Ranbir Singh Pura, India
| | - Simrinder Singh Sodhi
- Department of Animal Biotechnology, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - Mukesh Kumar Gupta
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, India
| | - Sung Jin Lee
- Department of Animal Biotechnology, College of Animal Life Sciences, Kangwon National University, Chuncheon-si, South Korea
| | - Young Ok Son
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju, South Korea
- *Correspondence: Neelesh Sharma, ; Young Ok Son,
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9
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Protein interaction networks define the genetic architecture of preterm birth. Sci Rep 2022; 12:438. [PMID: 35013336 PMCID: PMC8748950 DOI: 10.1038/s41598-021-03427-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
The likely genetic architecture of complex diseases is that subgroups of patients share variants in genes in specific networks sufficient to express a shared phenotype. We combined high throughput sequencing with advanced bioinformatic approaches to identify such subgroups of patients with variants in shared networks. We performed targeted sequencing of patients with 2 or 3 generations of preterm birth on genes, gene sets and haplotype blocks that were highly associated with preterm birth. We analyzed the data using a multi-sample, protein–protein interaction (PPI) tool to identify significant clusters of patients associated with preterm birth. We identified shared protein interaction networks among preterm cases in two statistically significant clusters, p < 0.001. We also found two small control-dominated clusters. We replicated these data on an independent, large birth cohort. Separation testing showed significant similarity scores between the clusters from the two independent cohorts of patients. Canonical pathway analysis of the unique genes defining these clusters demonstrated enrichment in inflammatory signaling pathways, the glucocorticoid receptor, the insulin receptor, EGF and B-cell signaling, These results support a genetic architecture defined by subgroups of patients that share variants in genes in specific networks and pathways which are sufficient to give rise to the disease phenotype.
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Reiss JD, Peterson LS, Nesamoney SN, Chang AL, Pasca AM, Marić I, Shaw GM, Gaudilliere B, Wong RJ, Sylvester KG, Bonifacio SL, Aghaeepour N, Gibbs RS, Stevenson DK. Perinatal infection, inflammation, preterm birth, and brain injury: A review with proposals for future investigations. Exp Neurol 2022; 351:113988. [DOI: 10.1016/j.expneurol.2022.113988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/06/2022] [Accepted: 01/13/2022] [Indexed: 11/26/2022]
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Huang W, Gu H, Yuan Z. Identifying biomarkers for prenatal diagnosis of neural tube defects based on "omics". Clin Genet 2021; 101:381-389. [PMID: 34761376 DOI: 10.1111/cge.14087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 11/27/2022]
Abstract
Neural tube defects (NTDs) are the most severe birth defects and the main cause of newborn death; posing a great challenge to the affected children, families, and societies. Presently, the clinical diagnosis of NTDs mainly relies on ultrasound images combined with certain indices, such as alpha-fetoprotein levels in the maternal serum and amniotic fluid. Recently, the discovery of additional biomarkers in maternal tissue has presented new possibilities for prenatal diagnosis. Over the past 20 years, "omics" techniques have provided the premise for the study of biomarkers. This review summarizes recent advances in candidate biomarkers for the prenatal diagnosis of fetal NTDs based on omics techniques using maternal biological specimens of different origins, including amniotic fluid, blood, and urine, which may provide a foundation for the early prenatal diagnosis of NTDs.
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Affiliation(s)
- Wanqi Huang
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, China
| | - Hui Gu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, China
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, China
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12
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Feng WW, Liu J, Cheng H, Peng C. Integration of Gut Microbiota and Metabolomics for Chinese Medicines Research: Opportunities and Challenges. Chin J Integr Med 2021; 28:1032-1039. [PMID: 34755290 DOI: 10.1007/s11655-021-3305-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2021] [Indexed: 12/15/2022]
Abstract
Chinese medicines (CM) are gaining more attentions from all over the world. However, there are a large body of questions to be answered because of the chemical complexity of CM and intricate molecular reactions within human body. In recent years, gut microbiota and metabolomics have emerged as two cynosures in deciphering the mechanisms of how our body is functioning. Since gut microbiota and host is a closely interrelated system, paying attention only to gut microbiota or metabolites may omit the interplays among CM, gut microbiota, and hosts. To systemically study these interplays, a network understanding of CM components, gut microbiota, metabolites of gut microbiota, metabolites in human body is necessary. Although there are some obstacles impeding the application of this integrative approach, the potential areas for implementation of the integrative approach is vast. These areas include, but not limited to, elucidating the mechanisms of CM at system level, screening bioactive compounds in CM, and guiding quality control of CM.
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Affiliation(s)
- Wu-Wen Feng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Juan Liu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Hao Cheng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Cheng Peng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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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 <34 weeks 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 32-34 weeks of gestation.Results: (1) Average expression of the 16-gene untargeted cellular mRNA signature was higher in women diagnosed with early preeclampsia at 32-34 weeks of gestation, yet more importantly, also prior to diagnosis at 28-32 weeks and 22-28 weeks of gestation, compared to controls (all, p < .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 22-28 weeks of gestation. (3) H19, FN1, and TUBB6 were increased in women with early preeclampsia as early as 11-17 weeks of gestation (all, p < .05). (4) After diagnosis at 32-34 weeks, but also prior to diagnosis at 11-17 weeks, 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, p < .05). (5) A combination of three mRNAs from the extravillous trophoblast signature (MMP11, SLC6A2, and IL18BP) predicted early preeclampsia at 11-17 weeks 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 22 weeks of gestation, and individual mRNAs of this signature were significantly increased as early as 11-17 weeks of gestation. Several single-cell placental signatures predicted future development of the disease at 11-17 weeks and were also increased in women already diagnosed at 32-34 weeks 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 “D,” 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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14
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Monangi N, Xu H, Khanam R, Khan W, Deb S, Pervin J, Price JT, Kennedy SH, Al Mahmud A, Fan Y, Le TQ, Care A, Landero JA, Combs GF, Belling E, Chappell J, Kong F, Lacher C, Ahmed S, Chowdhury NH, Rahman S, Kabir F, Nisar I, Hotwani A, Mehmood U, Nizar A, Khalid J, Dhingra U, Dutta A, Ali S, Aftab F, Juma MH, Rahman M, Vwalika B, Musonda P, Ahmed T, Islam MM, Ashorn U, Maleta K, Hallman M, Goodfellow L, Gupta JK, Alfirevic A, Murphy S, Rand L, Ryckman KK, Murray JC, Bahl R, Litch JA, Baruch-Gravett C, Alfirevic Z, Ashorn P, Baqui A, Hirst J, Hoyo C, Jehan F, Jelliffe-Pawlowski LL, Rahman A, Roth DE, Sazawal S, Stringer J, Zhang G, Muglia L. Association of maternal prenatal selenium concentration and preterm birth: a multicountry meta-analysis. BMJ Glob Health 2021; 6:bmjgh-2021-005856. [PMID: 34518202 PMCID: PMC8438754 DOI: 10.1136/bmjgh-2021-005856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/04/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Selenium (Se), an essential trace mineral, has been implicated in preterm birth (PTB). We aimed to determine the association of maternal Se concentrations during pregnancy with PTB risk and gestational duration in a large number of samples collected from diverse populations. METHODS Gestational duration data and maternal plasma or serum samples of 9946 singleton live births were obtained from 17 geographically diverse study cohorts. Maternal Se concentrations were determined by inductively coupled plasma mass spectrometry analysis. The associations between maternal Se with PTB and gestational duration were analysed using logistic and linear regressions. The results were then combined using fixed-effect and random-effect meta-analysis. FINDINGS In all study samples, the Se concentrations followed a normal distribution with a mean of 93.8 ng/mL (SD: 28.5 ng/mL) but varied substantially across different sites. The fixed-effect meta-analysis across the 17 cohorts showed that Se was significantly associated with PTB and gestational duration with effect size estimates of an OR=0.95 (95% CI: 0.9 to 1.00) for PTB and 0.66 days (95% CI: 0.38 to 0.94) longer gestation per 15 ng/mL increase in Se concentration. However, there was a substantial heterogeneity among study cohorts and the random-effect meta-analysis did not achieve statistical significance. The largest effect sizes were observed in UK (Liverpool) cohort, and most significant associations were observed in samples from Malawi. INTERPRETATION While our study observed statistically significant associations between maternal Se concentration and PTB at some sites, this did not generalise across the entire cohort. Whether population-specific factors explain the heterogeneity of our findings warrants further investigation. Further evidence is needed to understand the biologic pathways, clinical efficacy and safety, before changes to antenatal nutritional recommendations for Se supplementation are considered.
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Affiliation(s)
- Nagendra Monangi
- Division of Neonatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Huan Xu
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Rasheda Khanam
- International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Waqasuddin Khan
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Saikat Deb
- Center for Public Health Kinetics, New Delhi, India
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Jesmin Pervin
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Dhaka District, Bangladesh
| | - Joan T Price
- Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Stephen H Kennedy
- INTERBIO-21st Study Consortium, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - Abdullah Al Mahmud
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Dhaka District, Bangladesh
| | - Yuemei Fan
- Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Pirkanmaa, Finland
| | - Thanh Q Le
- Benh Vien Tu Du, Ho Chi Minh City, Viet Nam
| | - Angharad Care
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - Julio A Landero
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Gerald F Combs
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Medford, Massachusetts, USA
| | - Elizabeth Belling
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Joanne Chappell
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Fansheng Kong
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Criag Lacher
- Grand Forks Human Nutrition Research Center, USDA ARS, Grand Forks, North Dakota, USA
| | | | | | | | - Furqan Kabir
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Imran Nisar
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Aneeta Hotwani
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Usma Mehmood
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Ambreen Nizar
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Javairia Khalid
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Usha Dhingra
- Center for Public Health Kinetics, New Delhi, India
| | - Arup Dutta
- Center for Public Health Kinetics, New Delhi, India
| | - Said Ali
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Fahad Aftab
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Mohammed Hamad Juma
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Monjur Rahman
- Nutritional and Clinical Services Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Dhaka District, Bangladesh
| | | | - Patrick Musonda
- School of Public Health, University of Zambia, Lusaka, Zambia
| | | | - Md Munirul Islam
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Ulla Ashorn
- University of Tampere, Tampere, Pirkanmaa, Finland
| | - Kenneth Maleta
- School of Public Health, University of Malawi College of Medicine, Blantyre, Malawi
| | - Mikko Hallman
- Medical Research Centre Oulu, PEDEGO Research Unit, University of Oulu, Oulu, Pohjois-Pohjanmaa, Finland
| | - Laura Goodfellow
- Department of Women's and Children's Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Juhi K Gupta
- Department of Women's and Children's Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Ana Alfirevic
- Department of Women's and Children's Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Susan Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Larry Rand
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
| | - Kelli K Ryckman
- Department of Epidemiology, University of Iowa, Iowa City, Iowa, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Rajiv Bahl
- Department of Medicine, World Health Organization, Geneva, Switzerland
| | - James A Litch
- Global Alliance to Prevent Prematurity and Stillbirth, Lynnwood, Washington, USA
| | | | - Zarko Alfirevic
- Division of Perinatal Medicine, University of Liverpool, Liverpool, UK
| | - Per Ashorn
- Center for Child Health Research, Faculty of Medicine and Health Technology, University of Tampere, Tampere, Pirkanmaa, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Abdullah Baqui
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jane Hirst
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Cathrine Hoyo
- Department of Biological Sciences and Center for Human Health and the Enivironment, North Carolina State University, Raleigh, North Carolina, USA
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Laura L Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Anisur Rahman
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Dhaka District, Bangladesh
| | - Daniel E Roth
- Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sunil Sazawal
- Center for Public Health Kinetics, New Delhi, India
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Jeffrey Stringer
- Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ge Zhang
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Louis Muglia
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Burroughs Wellcome Fund, Research Triangle Park, North Carolina, USA
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15
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Orr TJ, Hayssen V. The Female Snark Is Still a Boojum: Looking toward the Future of Studying Female Reproductive Biology. Integr Comp Biol 2021; 60:782-795. [PMID: 32702114 DOI: 10.1093/icb/icaa091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Philosophical truths are hidden in Lewis Carroll's nonsense poems, such as "The hunting of the snark." When the poem is used as a scientific allegory, a snark stands for the pursuit of scientific truth, while a boojum is a spurious discovery. In the study of female biology, boojums have been the result of the use of cultural stereotypes to frame hypotheses and methodologies. Although female reproduction is key for the continuation of sexually reproducing species, not only have females been understudied in many regards, but also data have commonly been interpreted in the context of now-outdated social mores. Spurious discoveries, boojums, are the result. In this article, we highlight specific gaps in our knowledge of female reproductive biology and provide a jumping-off point for future research. We discuss the promise of emerging methodologies (e.g., micro-CT scanning, high-throughput sequencing, proteomics, big-data analysis, CRISPR-Cas9, and viral vector technology) that can yield insights into previously cryptic processes and features. For example, in mice, deoxyribonucleic acid sequencing via chromatin immunoprecipitation followed by sequencing is already unveiling how epigenetics lead to sex differences in brain development. Similarly, new explorations, including microbiome research, are rapidly debunking dogmas such as the notion of the "sterile womb." Finally, we highlight how understanding female reproductive biology is well suited to the National Science Foundation's big idea, "Predicting Rules of Life." Studies of female reproductive biology will enable scholars to (1) traverse levels of biological organization from reproductive proteins at the molecular level, through anatomical details of the ovum and female reproductive tract, into physiological aspects of whole-organism performance, leading to behaviors associated with mating and maternal care, and eventually reaching population structure and ecology; (2) discover generalizable rules such as the co-evolution of maternal-offspring phenotypes in gestation and lactation; and (3) predict the impacts of changes to reproductive timing when the reliability of environmental cues becomes unpredictable. Studies in these key areas relative to female reproduction are sure to further our understanding across a range of diverse taxa.
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Affiliation(s)
- Teri J Orr
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Virginia Hayssen
- Department of Biological Sciences, Smith College, Northampton, MA, USA
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16
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Tarca AL, Pataki BÁ, Romero R, Sirota M, Guan Y, Kutum R, Gomez-Lopez N, Done B, Bhatti G, Yu T, Andreoletti G, Chaiworapongsa T, Hassan SS, Hsu CD, Aghaeepour N, Stolovitzky G, Csabai I, Costello JC. Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth. Cell Rep Med 2021; 2:100323. [PMID: 34195686 PMCID: PMC8233692 DOI: 10.1016/j.xcrm.2021.100323] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/18/2021] [Accepted: 05/20/2021] [Indexed: 12/15/2022]
Abstract
Identification of pregnancies at risk of preterm birth (PTB), the leading cause of newborn deaths, remains challenging given the syndromic nature of the disease. We report a longitudinal multi-omics study coupled with a DREAM challenge to develop predictive models of PTB. The findings indicate that whole-blood gene expression predicts ultrasound-based gestational ages in normal and complicated pregnancies (r = 0.83) and, using data collected before 37 weeks of gestation, also predicts the delivery date in both normal pregnancies (r = 0.86) and those with spontaneous preterm birth (r = 0.75). Based on samples collected before 33 weeks in asymptomatic women, our analysis suggests that expression changes preceding preterm prelabor rupture of the membranes are consistent across time points and cohorts and involve leukocyte-mediated immunity. Models built from plasma proteomic data predict spontaneous preterm delivery with intact membranes with higher accuracy and earlier in pregnancy than transcriptomic models (AUROC = 0.76 versus AUROC = 0.6 at 27-33 weeks of gestation).
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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, US Department of Health and Human Services, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201 USA
- Department of Computer Science, Wayne State University College of Engineering, Detroit, MI 48202, USA
| | - Bálint Ármin Pataki
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - 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, US Department of Health and Human Services, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Detroit Medical Center, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Florida International University, Miami, FL 33199, USA
| | - Marina Sirota
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rintu Kutum
- Informatics and Big Data Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - 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, US Department of Health and Human Services, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201 USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI 48201 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, US Department of Health and Human Services, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201 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, US Department of Health and Human Services, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | | | - Gaia Andreoletti
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tinnakorn Chaiworapongsa
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | - The DREAM Preterm Birth Prediction Challenge Consortium
- 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, US Department of Health and Human Services, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201 USA
- Department of Computer Science, Wayne State University College of Engineering, Detroit, MI 48202, USA
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Detroit Medical Center, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Florida International University, Miami, FL 33199, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Informatics and Big Data Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI 48201 USA
- Sage Bionetworks, Seattle, WA, USA
- Office of Women’s Health, Integrative Biosciences Center, Wayne State University, Detroit, MI 48202, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Department of Pediatrics, and Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, USA
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sonia S. Hassan
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201 USA
- Office of Women’s Health, Integrative Biosciences Center, Wayne State University, Detroit, MI 48202, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, 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, US Department of Health and Human Services, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201 USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative, and Pain Medicine, Department of Pediatrics, and Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gustavo Stolovitzky
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Istvan Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - James C. Costello
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Turkmen S, Bäckström T, Kangas Flodin Y, Bixo M. Neurosteroid involvement in threatened preterm labour. Endocrinol Diabetes Metab 2021; 4:e00216. [PMID: 33855217 PMCID: PMC8029533 DOI: 10.1002/edm2.216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 12/02/2022] Open
Abstract
Introduction The neurosteroid allopregnanolone modulates oxytocin expression in the brain, and its effects arise from its action on the GABAA receptor. Whether neurosteroid levels and the function of the GABAA receptor are involved in the risk of preterm labour in pregnant women is unknown. Methods Pregnant women with (n = 16) or without (n = 20) threatened preterm labour (TPL) in gestational week 33 + 6 days to 37 + 0 days were studied prospectively with procedures including foetal heart rate monitoring, vaginal examination, ultrasound examination and blood tests to determine allopregnanolone, progesterone and oxytocin levels. The GABAA receptor function in both groups was measured with a saccadic eye velocity test (SEVT). Results Plasma oxytocin levels were higher in the TPL group than in the control group (41.5 vs. 37.0 pmol/L, respectively, p = .021). Although the allopregnanolone and progesterone levels in both groups did not differ, there was a negative association between blood oxytocin and allopregnanolone (as predictor) levels in the TPL group (B: -3.2, 95% confidence interval (CI): -5.5 to -0.9, p = .012). As a predictor of TPL, progesterone was associated with cervix maturity (odds ratio: 1.02, 95% CI: 1.00-1.04, p = .038). SEVT showed that the women in both groups had similar GABAA receptor functions. In both groups, body mass index correlated with peak saccadic eye velocity (r = .34, p = .044) and negatively with allopregnanolone (r = -.41, p = .013). Conclusions Neurosteroid levels were unchanged in the peripheral blood of women with TPL, despite the increase in available oxytocin. Although the function of the GABAA receptor was unchanged in women with TPL, to ensure reliable results, saccadic eye velocity should be investigated during a challenge test with a GABAA receptor agonist.
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Affiliation(s)
- Sahruh Turkmen
- Sundsvalls Research UnitDepartment of Clinical Sciences, Obstetrics and GynaecologyUmeå UniversitySundsvallSweden
| | - Torbjörn Bäckström
- Sundsvalls Research UnitDepartment of Clinical Sciences, Obstetrics and GynaecologyUmeå UniversitySundsvallSweden
| | - Yvonne Kangas Flodin
- Sundsvalls Research UnitDepartment of Clinical Sciences, Obstetrics and GynaecologyUmeå UniversitySundsvallSweden
| | - Marie Bixo
- Sundsvalls Research UnitDepartment of Clinical Sciences, Obstetrics and GynaecologyUmeå UniversitySundsvallSweden
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Chalupska M, Kacerovsky M, Stranik J, Gregor M, Maly J, Jacobsson B, Musilova I. Intra-Amniotic Infection and Sterile Intra-Amniotic Inflammation in Cervical Insufficiency with Prolapsed Fetal Membranes: Clinical Implications. Fetal Diagn Ther 2020; 48:58-69. [PMID: 33291113 DOI: 10.1159/000512102] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/05/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION The aim of this study was to identify the rates of 2 phenotypes of intra-amniotic inflammation: intra-amniotic infection (with microbial invasion of the amniotic cavity [MIAC]) and sterile intra-amniotic inflammation (without MIAC), and their outcomes, among women with cervical insufficiency with prolapsed fetal membranes. METHODS OF STUDY This is a retrospective study of women admitted to the Department of Obstetrics and Gynecology, University Hospital Hradec Kralove between January 2014 and May 2020. Transabdominal amniocentesis to evaluate intra-amniotic inflammation (amniotic fluid interleukin-6) and MIAC (culturing and molecular biology methods) was performed as part of standard clinical management. RESULTS In total, 37 women with cervical insufficiency and prolapsed fetal membranes were included; 11% (4/37) and 43% (16/37) of them had intra-amniotic infection and sterile intra-amniotic inflammation, respectively. In women with intra-amniotic infection and sterile intra-amniotic inflammation, we noted shorter intervals between admission and delivery (both p < 0.0001), and lower gestational age at delivery (p < 0.0001 and p = 0.004) and percentiles of birth/abortion weight (p = 0.03 and p = 0.009, respectively) than in those without intra-amniotic inflammation. CONCLUSIONS Both phenotypes of intra-amniotic inflammation, with sterile intra-amniotic inflammation being more frequent, are associated with worse outcomes in pregnancies with cervical insufficiency with prolapsed fetal membranes.
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Affiliation(s)
- Martina Chalupska
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Hradec Kralove, Czechia
| | - Marian Kacerovsky
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Hradec Kralove, Czechia, .,Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czechia,
| | - Jaroslav Stranik
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Hradec Kralove, Czechia
| | - Miroslav Gregor
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Hradec Kralove, Czechia
| | - Jan Maly
- Department of Pediatrics, University Hospital Hradec Kralove, Hradec Kralove, Czechia
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Genetics and Bioinformatics, Domain of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Ivana Musilova
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Hradec Kralove, Czechia
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Li W, Chung CYL, Wang CC, Chan TF, Leung MBW, Chan OK, Wu L, Appiah K, Chaemsaithong P, Cheng YKY, Poon LCY, Leung TY. Monochorionic twins with selective fetal growth restriction: insight from placental whole-transcriptome analysis. Am J Obstet Gynecol 2020; 223:749.e1-749.e16. [PMID: 32437666 DOI: 10.1016/j.ajog.2020.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/24/2020] [Accepted: 05/05/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND The underlying pathomechanism in placenta-related selective fetal growth restriction in monochorionic diamniotic twin pregnancy is not known. OBJECTIVE This study aimed to investigate any differences in placental transcriptomic profile between the selectively growth-restricted twins and the normally grown cotwins in monochorionic diamniotic twin pregnancies. STUDY DESIGN This was a prospective study of monochorionic diamniotic twin pregnancies complicated by selective fetal growth restriction. Placental biopsy specimens were obtained from the subjects in the delivery suite. The placental transcriptome of the selectively growth-restricted twin was compared with that of the normally grown cotwin. This study was divided into 2 stages: (1) gene discovery phase in which placental tissues from 5 monochorionic diamniotic twin pregnancies complicated by selective fetal growth restriction plus 2 control twin pregnancies underwent transcriptome profiling, and transcriptome profiling was carried out using whole-genome RNA sequencing; and (2) validation phase in which placental tissues from 13 monochorionic diamniotic twin pregnancies with selective fetal growth restriction underwent RNA and protein validation. RNA and protein expression levels of candidate genes were determined using quantitative real-time polymerase chain reaction and immunohistochemistry staining. RESULTS A total of 1429 transcripts were differentially expressed in the placentae of selectively growth-restricted twin pairs, where 610 were up-regulated and 819 were down-regulated. Endoplasmic reticulum lectin and mannose 6-phosphate receptor were consistently differentially up-regulated in all placentae of selectively growth-restricted twins. Quantitative real-time polymerase chain reaction and immunohistochemistry staining were used to validate the results (P<.05). CONCLUSION The expression of endoplasmic reticulum lectin and mannose 6-phosphate receptor, which are important for angiogenesis and fetal growth, was significantly increased in the placentae of selectively growth-restricted twin of a monochorionic twin pair.
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Affiliation(s)
- Wei Li
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Claire Yik Lok Chung
- School of Life Sciences, the Chinese University of Hong Kong, Shatin, Hong Kong; Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chi Chiu Wang
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong; Department of Reproduction and Development, Li Ka Shing Institute of Health Sciences, the Chinese University of Hong Kong, Shatin, Hong Kong; School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ting Fung Chan
- School of Life Sciences, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Maran Bo Wah Leung
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Oi Ka Chan
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong; Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ling Wu
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kubi Appiah
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Piya Chaemsaithong
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yvonne Kwun Yue Cheng
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Liona Chiu Yee Poon
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong.
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20
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Gil-de-Gómez L, Balgoma D, Montero O. Lipidomic-Based Advances in Diagnosis and Modulation of Immune Response to Cancer. Metabolites 2020; 10:metabo10080332. [PMID: 32824009 PMCID: PMC7465074 DOI: 10.3390/metabo10080332] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023] Open
Abstract
While immunotherapies for diverse types of cancer are effective in many cases, relapse is still a lingering problem. Like tumor cells, activated immune cells have an anabolic metabolic profile, relying on glycolysis and the increased uptake and synthesis of fatty acids. In contrast, immature antigen-presenting cells, as well as anergic and exhausted T-cells have a catabolic metabolic profile that uses oxidative phosphorylation to provide energy for cellular processes. One goal for enhancing current immunotherapies is to identify metabolic pathways supporting the immune response to tumor antigens. A robust cell expansion and an active modulation via immune checkpoints and cytokine release are required for effective immunity. Lipids, as one of the main components of the cell membrane, are the key regulators of cell signaling and proliferation. Therefore, lipid metabolism reprogramming may impact proliferation and generate dysfunctional immune cells promoting tumor growth. Based on lipid-driven signatures, the discrimination between responsiveness and tolerance to tumor cells will support the development of accurate biomarkers and the identification of potential therapeutic targets. These findings may improve existing immunotherapies and ultimately prevent immune escape in patients for whom existing treatments have failed.
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Affiliation(s)
- Luis Gil-de-Gómez
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Colket Translational Research Center, 3501 Civic Center Blvd, PA 19104, USA
- Correspondence:
| | - David Balgoma
- Analytical Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University, Husarg. 3, 75123 Uppsala, Sweden;
| | - Olimpio Montero
- Spanish National Research Council (CSIC), Boecillo’s Technological Park Bureau, Av. Francisco Vallés 8, 47151 Boecillo, Spain;
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21
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Hallingström M, Zedníková P, Tambor V, Barman M, Vajrychová M, Lenčo J, Viklund F, Tancred L, Rabe H, Jonsson D, Kachikis A, Nilsson S, Kacerovský M, Adams Waldorf KM, Jacobsson B. Mid-trimester amniotic fluid proteome's association with spontaneous preterm delivery and gestational duration. PLoS One 2020; 15:e0232553. [PMID: 32379834 PMCID: PMC7205297 DOI: 10.1371/journal.pone.0232553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/16/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Amniotic fluid is clinically accessible via amniocentesis and its protein composition may correspond to birth timing. Early changes in the amniotic fluid proteome could therefore be associated with the subsequent development of spontaneous preterm delivery. OBJECTIVE The main objective of this study was to perform unbiased proteomics analysis of the association between mid-trimester amniotic fluid proteome and spontaneous preterm delivery and gestational duration, respectively. A secondary objective was to validate and replicate the findings by enzyme-linked immunosorbent assay using a second independent cohort. METHODS Women undergoing a mid-trimester genetic amniocentesis at Sahlgrenska University Hospital/Östra between September 2008 and September 2011 were enrolled in this study, designed in three analytical stages; 1) an unbiased proteomic discovery phase using LC-MS analysis of 22 women with subsequent spontaneous preterm delivery (cases) and 37 women who delivered at term (controls), 2) a validation phase of proteins of interest identified in stage 1, and 3) a replication phase of the proteins that passed validation using a second independent cohort consisting of 20 cases and 40 matched controls. RESULTS Nine proteins were nominally significantly associated with both spontaneous preterm delivery and gestational duration, after adjustment for gestational age at sampling, but none of the proteins were significant after correction for multiple testing. Several of these proteins have previously been described as being associated with spontaneous PTD etiology and six of them were thus validated using enzyme linked immunosorbent assay. Two of the proteins passed validation; Neutrophil gelatinase-associated lipocalin and plasminogen activator inhibitor 1, but the results could not be replicated in a second cohort. CONCLUSIONS Neutrophil gelatinase-associated lipocalin and Plasminogen activator inhibitor 1 are potential biomarkers of spontaneous preterm delivery and gestational duration but the findings could not be replicated. The negative findings are supported by the fact that none of the nine proteins from the exploratory phase were significant after correction for multiple testing.
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Affiliation(s)
- Maria Hallingström
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Petra Zedníková
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Biological and Biochemical Science, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Vojtěch Tambor
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Malin Barman
- Department of Biology and Biological Engineering, Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
| | - Marie Vajrychová
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defense, Hradec Kralove, Czech Republic
| | - Juraj Lenčo
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Hradec Kralove, Czech Republic
| | - Felicia Viklund
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Stockholm South General Hospital, Stockholm, Sweden
| | - Linda Tancred
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Biobank Väst, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Hardis Rabe
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Jonsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Alisa Kachikis
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Staffan Nilsson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marian Kacerovský
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Obstetrics and Gynecology, Charles University in Prague, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Kristina M. Adams Waldorf
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Area of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
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El-Sheikh Ali H, Boakari YL, Loux SC, Dini P, Scoggin KE, Esteller-Vico A, Kalbfleisch T, Ball BA. Transcriptomic analysis reveals the key regulators and molecular mechanisms underlying myometrial activation during equine placentitis†. Biol Reprod 2020; 102:1306-1325. [PMID: 32065222 DOI: 10.1093/biolre/ioaa020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/30/2020] [Accepted: 02/14/2020] [Indexed: 01/06/2023] Open
Abstract
The key event in placentitis-induced preterm labor is myometrial activation with the subsequent initiation of labor. However, the molecular mechanisms underlying myometrial activation are not fully understood in the mares. Therefore, the equine myometrial transcriptome was characterized during placentitis (290.0 ± 1.52 days of GA, n = 5) and the prepartum period (330 days of GA, n = 3) in comparison to normal pregnant mares (289.8 ± 2.18 days of GA, n = 4). Transcriptome analysis identified 596 and 290 DEGs in the myometrium during placentitis and the prepartum period, respectively, with 138 DEGs in common. The placentitis DEGs included eight genes (MMP1, MMP8, S100A9, S100A8, PI3, APOBEC3Z1B, RETN, and CXCL2) that are exclusively expressed in the inflamed myometrium. Pathway analysis elucidated that inflammatory signaling, Toll-like receptor signaling, and apoptosis pathways dominate myometrial activation during placentitis. The prepartum myometrium was associated with overexpression of inflammatory signaling, oxidative stress, and 5-hydroxytryptamine degradation. Gene ontology enrichment analysis identified several chemoattractant factors in the myometrium during placentitis and prepartum period, including CCL2, CXCL1, CXCL3, and CXCL6 in common. Upstream regulator analysis revealed 19 potential upstream regulators in placentitis dataset including transcription regulators (E2F1, FOXM1, HIF1A, JUNB, NFKB1A, and STAT1), transmembrane receptors (FAS, ICAM1, SELP, TLR2, and TYROBP), growth factors (HGF and TGFB3), enzymes (PTGS2 and PRKCP), and others (S100A8, S100A9, CD44, and C5AR1). Additionally, three upstream regulators (STAT3, EGR1, and F2R) were identified in the prepartum dataset. These findings revealed the key regulators and pathways underlying myometrial activation during placentitis, which aid in understanding the disease and facilitate the development of efficacious therapies.
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Affiliation(s)
- H El-Sheikh Ali
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA.,Theriogenology Department, Faculty of Veterinary Medicine, University of Mansoura, Dakahlia, Mansoura, Egypt
| | - Y L Boakari
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - S C Loux
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - P Dini
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA.,Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - K E Scoggin
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - A Esteller-Vico
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA.,Department of Biomedical and Diagnostic Sciences, University of Tennessee, Tennessee, Knoxville, USA
| | - T Kalbfleisch
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - B A Ball
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
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23
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Tian JS, Qin XM, Gao Y, Zhao YX, Xu T. Research progress on antidepressant therapeutic biomarkers of xiaoyaosan. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2020. [DOI: 10.4103/wjtcm.wjtcm_16_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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24
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Li X, Peng T, Mu L, Hu X. Phytotoxicity induced by engineered nanomaterials as explored by metabolomics: Perspectives and challenges. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 184:109602. [PMID: 31493589 DOI: 10.1016/j.ecoenv.2019.109602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Given the wide applications of engineered nanomaterials (ENMs) in various fields, the ecotoxicology of ENMs has attracted much attention. The traditional plant physiological activity (e.g., reactive oxygen species and antioxidant enzymes) are limited in that they probe one specific process of nanotoxicity, which may result in the loss of understanding of other important biological reactions. Metabolites, which are downstream of gene and protein expression, are directly related to biological phenomena. Metabolomics is an easily performed and efficient tool for solving the aforementioned problems because it involves the comprehensive exploration of metabolic profiles. To understand the roles of metabolomics in phytotoxicity, the analytical methods for metabolomics should be organized and discussed. Moreover, the dominant metabolites and metabolic pathways are similar in different plants, which determines the universal applicability of metabolomics analysis. The analysis of regulated metabolism will globally and scientifically help determine the ecotoxicology that is induced by ENMs. In the past several years, great developments in nanotoxicology have been achieved using metabolomics. However, many knowledge gaps remain, such as the relationships between biological responses that are induced by ENMs and the regulation of metabolism (e.g., carbohydrate, energy, amino acid, lipid and secondary metabolism). The phytotoxicity that is induced by ENMs has been explored by metabolomics, which is still in its infancy. The detrimental and defence mechanisms of plants in their response to ENMs at the level of metabolomics also deserve much attention. In addition, owing to the regulation of metabolism in plants by ENMs affected by multiple factors, it is meaningful to uniformly identify the key influencing factor.
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Affiliation(s)
- Xiaokang Li
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Ting Peng
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Li Mu
- Tianjin Key Laboratory of Agro-environment and Safe-product, Key Laboratory for Environmental Factors Control of Agro-product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-environmental Protection, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
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25
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Handelman SK, Romero R, Tarca AL, Pacora P, Ingram B, Maymon E, Chaiworapongsa T, Hassan SS, Erez O. The plasma metabolome of women in early pregnancy differs from that of non-pregnant women. PLoS One 2019; 14:e0224682. [PMID: 31726468 PMCID: PMC6855901 DOI: 10.1371/journal.pone.0224682] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/18/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In comparison to the non-pregnant state, the first trimester of pregnancy is characterized by systemic adaptation of the mother. The extent to which these adaptive processes are reflected in the maternal blood metabolome is not well characterized. OBJECTIVE To determine the differences between the plasma metabolome of non-pregnant and pregnant women before 16 weeks gestation. STUDY DESIGN This study included plasma samples from 21 non-pregnant women and 50 women with a normal pregnancy (8-16 weeks of gestation). Combined measurements by ultrahigh performance liquid chromatography/tandem mass spectrometry and by gas chromatography/mass spectrometry generated molecular abundance measurements for each sample. Molecular species detected in at least 10 samples were included in the analysis. Differential abundance was inferred based on false discovery adjusted p-values (FDR) from Mann-Whitney-Wilcoxon U tests <0.1 and a minimum median abundance ratio (fold change) of 1.5. Alternatively, metabolic data were quantile normalized to remove sample-to-sample differences in the overall metabolite abundance (adjusted analysis). RESULTS Overall, 637 small molecules met the inclusion criteria and were tested for association with pregnancy; 44% (281/637) of small molecules had significantly different abundance, of which 81% (229/281) were less abundant in pregnant than in non-pregnant women. Eight percent (14/169) of the metabolites that remained significant in the adjusted analysis also changed as a function of gestational age. A pathway analysis revealed enrichment in steroid metabolites related to sex hormones, caffeine metabolites, lysolipids, dipeptides, and polypeptide bradykinin derivatives (all, FDR < 0.1). CONCLUSIONS This high-throughput mass spectrometry study identified: 1) differences between pregnant vs. non-pregnant women in the abundance of 44% of the profiled plasma metabolites, including known and novel molecules and pathways; and 2) specific metabolites that changed with gestational age.
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Affiliation(s)
- Samuel K. Handelman
- 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, United States of America
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
- Detroit Medical Center, Detroit, Michigan, United States of America
| | - 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Computer Science, Wayne State University College of Engineering, Detroit, Michigan, United States of America
| | - 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Brian Ingram
- Metabolon Inc., Raleigh-Durham, North Carolina, United States of America
| | - Eli Maymon
- 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Soroka University Medical Center, School of Medicine, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tinnakorn Chaiworapongsa
- 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Offer Erez
- 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Maternity Department "D," 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
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Souza RT, McKenzie EJ, Jones B, de Seymour JV, Thomas MM, Zarate E, Han TL, McCowan L, Sulek K, Villas-Boas S, Kenny LC, Cecatti JG, Baker PN. Trace biomarkers associated with spontaneous preterm birth from the maternal serum metabolome of asymptomatic nulliparous women - parallel case-control studies from the SCOPE cohort. Sci Rep 2019; 9:13701. [PMID: 31548567 PMCID: PMC6757051 DOI: 10.1038/s41598-019-50252-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 09/09/2019] [Indexed: 02/07/2023] Open
Abstract
Prediction of spontaneous preterm birth (sPTB) in asymptomatic women remains a great challenge; accurate and reproducible screening tools are still not available in clinical practice. We aimed to investigate whether the maternal serum metabolome together with clinical factors could be used to identify asymptomatic women at risk of sPTB. We conducted two case-control studies using gas chromatography-mass spectrometry to analyse maternal serum samples collected at 15- and 20-weeks' gestation from 164 nulliparous women from Cork, and 157 from Auckland. Smoking and vaginal bleeding before 15 weeks were the only significant clinical predictors of sPTB for Auckland and Cork subsets, respectively. Decane, undecane, and dodecane were significantly associated with sPTB (FDR < 0.05) in the Cork subset. An odds ratio of 1.9 was associated with a one standard deviation increase in log (undecane) in a multiple logistic regression which also included vaginal bleeding as a predictor. In summary, elevated serum levels of the alkanes decane, undecane, and dodecane were associated with sPTB in asymptomatic nulliparous women from Cork, but not in the Auckland cohort. The association is not strong enough to be a useful clinical predictor, but suggests that further investigation of the association between oxidative stress processes and sPTB risk is warranted.
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Affiliation(s)
- Renato T Souza
- Department of Obstetrics and Gynecology, University of Campinas, Campinas, Brazil.
| | | | | | | | | | - Erica Zarate
- The University of Auckland, Auckland, New Zealand
| | - Ting Li Han
- The University of Auckland, Auckland, New Zealand
| | | | | | | | - Louise C Kenny
- The Department of Women's and Children's Health, Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - José G Cecatti
- Department of Obstetrics and Gynecology, University of Campinas, Campinas, Brazil
| | - Philip N Baker
- The University of Auckland, Auckland, New Zealand
- College of Life Sciences, University of Leicester, Leicester, United Kingdom
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27
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Philpot PA, Bhandari V. Predicting the likelihood of bronchopulmonary dysplasia in premature neonates. Expert Rev Respir Med 2019; 13:871-884. [PMID: 31340666 DOI: 10.1080/17476348.2019.1648215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Introduction: Bronchopulmonary dysplasia (BPD) is the most common serious pulmonary morbidity in premature infants. Despite ongoing advances in neonatal care, the incidence of BPD has not improved. A potential explanation for this phenomenon is the limited ability for accurate early prediction of the risk of BPD. BPD continues to represent a therapeutic challenge and no single effective therapy exists for this condition. Areas covered: Here, we review risk factors of BPD derived from clinical data, biological fluid biomarkers, respiratory management data, and scientific advancements using 'omics' technologies, and their ability to predict the pathogenesis of BPD in preterm neonates. Risk factors and biomarkers were identified via literature search with a focus on the last 5 years of data. Expert opinion: The most accurate predictive tools utilize risk factors that encompass a variety of categories. Numerous predictive models have been proposed but suffer from a lack of adequate validation. An ideal model should include multiple, easily measurable variables validated across a heterogeneous population. In addition to evaluating recent BPD prediction models, we suggest approaches to enhance future models.
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Affiliation(s)
- Patrick A Philpot
- Section of Neonatal-Perinatal Medicine, Department of Pediatrics, Thomas Jefferson University College of Medicine, Nemours/Alfred I. DuPont Hospital for Children , Philadelphia , PA , USA
| | - Vineet Bhandari
- Section of Neonatal-Perinatal Medicine, Department of Pediatrics, Drexel University College of Medicine, St. Christopher's Hospital for Children , Philadelphia , PA , USA
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28
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Faundez V, Wynne M, Crocker A, Tarquinio D. Molecular Systems Biology of Neurodevelopmental Disorders, Rett Syndrome as an Archetype. Front Integr Neurosci 2019; 13:30. [PMID: 31379529 PMCID: PMC6650571 DOI: 10.3389/fnint.2019.00030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022] Open
Abstract
Neurodevelopmental disorders represent a challenging biological and medical problem due to their genetic and phenotypic complexity. In many cases, we lack the comprehensive understanding of disease mechanisms necessary for targeted therapeutic development. One key component that could improve both mechanistic understanding and clinical trial design is reliable molecular biomarkers. Presently, no objective biological markers exist to evaluate most neurodevelopmental disorders. Here, we discuss how systems biology and "omic" approaches can address the mechanistic and biomarker limitations in these afflictions. We present heuristic principles for testing the potential of systems biology to identify mechanisms and biomarkers of disease in the example of Rett syndrome, a neurodevelopmental disorder caused by a well-defined monogenic defect in methyl-CpG-binding protein 2 (MECP2). We propose that such an approach can not only aid in monitoring clinical disease severity but also provide a measure of target engagement in clinical trials. By deepening our understanding of the "big picture" of systems biology, this approach could even help generate hypotheses for drug development programs, hopefully resulting in new treatments for these devastating conditions.
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Affiliation(s)
- Victor Faundez
- Department of Cell Biology, Emory University, Atlanta, GA, United States
| | - Meghan Wynne
- Department of Cell Biology, Emory University, Atlanta, GA, United States
| | - Amanda Crocker
- Program in Neuroscience, Middlebury College, Middlebury, VT, United States
| | - Daniel Tarquinio
- Rare Neurological Diseases (Private Research Institution), Atlanta, GA, United States
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29
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Szenasi NL, Toth E, Balogh A, Juhasz K, Karaszi K, Ozohanics O, Gelencser Z, Kiraly P, Hargitai B, Drahos L, Hupuczi P, Kovalszky I, Papp Z, Than NG. Proteomic identification of membrane-associated placental protein 4 (MP4) as perlecan and characterization of its placental expression in normal and pathologic pregnancies. PeerJ 2019; 7:e6982. [PMID: 31259093 PMCID: PMC6589330 DOI: 10.7717/peerj.6982] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/18/2019] [Indexed: 12/16/2022] Open
Abstract
Background More than 50 human placental proteins were isolated and physico-chemically characterized in the 70–80s by Hans Bohn and co-workers. Many of these proteins turned to have important role in placental functions and diagnostic significance in pregnancy complications. Among these proteins was membrane-associated placental protein 4 (MP4), for which identity or function has not been identified yet. Our aim was to analyze the sequence and placental expression of this protein in normal and complicated pregnancies including miscarriage, preeclampsia and HELLP syndrome. Methods Lyophilized MP4 protein and frozen healthy placental tissue were analyzed using HPLC-MS/MS. Placental tissue samples were obtained from women with elective termination of pregnancy (first trimester controls, n = 31), early pregnancy loss (EPL) (n = 13), early preeclampsia without HELLP syndrome (n = 7) and with HELLP syndrome (n = 8), late preeclampsia (n = 8), third trimester early controls (n = 5) and third trimester late controls (n = 9). Tissue microarrays were constructed from paraffin-embedded placentas (n = 81). Slides were immunostained with monoclonal perlecan antibody and evaluated using light microscopy and virtual microscopy. Perlecan was also analyzed for its expression in placentas from normal pregnancies using microarray data. Results Mass spectrometry-based proteomics of MP4 resulted in the identification of basement membrane-specific heparan sulfate proteoglycan core protein also known as perlecan. Immunohistochemistry showed cytoplasmic perlecan localization in syncytiotrophoblast and cytotrophoblasts of the villi. Perlecan immunoscore decreased with gestational age in the placenta. Perlecan immunoscores were higher in EPL compared to controls. Perlecan immunoscores were higher in early preeclampsia without and with HELLP syndrome and lower in late preeclampsia than in respective controls. Among patients with preeclampsia, placental perlecan expression positively correlated with maternal vascular malperfusion and negatively correlated with placental weight. Conclusion Our findings suggest that an increased placental perlecan expression may be associated with hypoxic ischaemic injury of the placenta in miscarriages and in early preeclampsia with or without HELLP syndrome.
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Affiliation(s)
- Nikolett Lilla Szenasi
- Systems Biology of Reproduction Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Eszter Toth
- Systems Biology of Reproduction Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.,MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Andrea Balogh
- Systems Biology of Reproduction Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kata Juhasz
- Systems Biology of Reproduction Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Katalin Karaszi
- 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
| | - Oliver Ozohanics
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Medical Biochemistry, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Zsolt Gelencser
- Systems Biology of Reproduction Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Peter Kiraly
- Systems Biology of Reproduction Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Beata Hargitai
- West Midlands Perinatal Pathology, Birmingham Women's Hospital, Birmingham, UK
| | - Laszlo Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Petronella Hupuczi
- Maternity Private Clinic of Obstetrics and Gynecology, Budapest, Hungary
| | - Ilona Kovalszky
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zoltan Papp
- Maternity Private Clinic of Obstetrics and Gynecology, Budapest, Hungary.,Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
| | - 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 Clinic of Obstetrics and Gynecology, Budapest, Hungary
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30
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Tarca AL, Romero R, Benshalom-Tirosh N, Than NG, Gudicha DW, Done B, Pacora P, Chaiworapongsa T, Panaitescu B, Tirosh D, Gomez-Lopez N, Draghici S, Hassan SS, Erez O. The prediction of early preeclampsia: Results from a longitudinal proteomics study. PLoS One 2019; 14:e0217273. [PMID: 31163045 PMCID: PMC6548389 DOI: 10.1371/journal.pone.0217273] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/08/2019] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES To identify maternal plasma protein markers for early preeclampsia (delivery <34 weeks of gestation) and to determine whether the prediction performance is affected by disease severity and presence of placental lesions consistent with maternal vascular malperfusion (MVM) among cases. STUDY DESIGN This longitudinal case-control study included 90 patients with a normal pregnancy and 33 patients with early preeclampsia. Two to six maternal plasma samples were collected throughout gestation from each woman. The abundance of 1,125 proteins was measured using high-affinity aptamer-based proteomic assays, and data were modeled using linear mixed-effects models. After data transformation into multiples of the mean values for gestational age, parsimonious linear discriminant analysis risk models were fit for each gestational-age interval (8-16, 16.1-22, 22.1-28, 28.1-32 weeks). Proteomic profiles of early preeclampsia cases were also compared to those of a combined set of controls and late preeclampsia cases (n = 76) reported previously. Prediction performance was estimated via bootstrap. RESULTS We found that 1) multi-protein models at 16.1-22 weeks of gestation predicted early preeclampsia with a sensitivity of 71% at a false-positive rate (FPR) of 10%. High abundance of matrix metalloproteinase-7 and glycoprotein IIbIIIa complex were the most reliable predictors at this gestational age; 2) at 22.1-28 weeks of gestation, lower abundance of placental growth factor (PlGF) and vascular endothelial growth factor A, isoform 121 (VEGF-121), as well as elevated sialic acid binding immunoglobulin-like lectin 6 (siglec-6) and activin-A, were the best predictors of the subsequent development of early preeclampsia (81% sensitivity, FPR = 10%); 3) at 28.1-32 weeks of gestation, the sensitivity of multi-protein models was 85% (FPR = 10%) with the best predictors being activated leukocyte cell adhesion molecule, siglec-6, and VEGF-121; 4) the increase in siglec-6, activin-A, and VEGF-121 at 22.1-28 weeks of gestation differentiated women who subsequently developed early preeclampsia from those who had a normal pregnancy or developed late preeclampsia (sensitivity 77%, FPR = 10%); 5) the sensitivity of risk models was higher for early preeclampsia with placental MVM lesions than for the entire early preeclampsia group (90% versus 71% at 16.1-22 weeks; 87% versus 81% at 22.1-28 weeks; and 90% versus 85% at 28.1-32 weeks, all FPR = 10%); and 6) the sensitivity of prediction models was higher for severe early preeclampsia than for the entire early preeclampsia group (84% versus 71% at 16.1-22 weeks). CONCLUSION We have presented herein a catalogue of proteome changes in maternal plasma proteome that precede the diagnosis of preeclampsia and can distinguish among early and late phenotypes. The sensitivity of maternal plasma protein models for early preeclampsia is higher in women with underlying vascular placental disease and in those with a severe phenotype.
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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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Computer Science, Wayne State University College of Engineering, Detroit, Michigan, United States of America
- * E-mail: (RR); (ALT)
| | - 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, United States of America
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
- * E-mail: (RR); (ALT)
| | - Neta Benshalom-Tirosh
- 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - 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 Clinic, Kutvolgyi Clinical Block, Semmelweis University, Budapest, Hungary
| | - Dereje W. Gudicha
- 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
| | - 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Tinnakorn Chaiworapongsa
- 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Bogdan Panaitescu
- 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Dan Tirosh
- 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan, United States of America
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Sorin Draghici
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Computer Science, Wayne State University College of Engineering, Detroit, Michigan, United States of America
| | - 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Offer Erez
- 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), Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Maternity Department "D," 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
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31
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Paquette AG, Brockway HM, Price ND, Muglia LJ. Comparative transcriptomic analysis of human placentae at term and preterm delivery. Biol Reprod 2019; 98:89-101. [PMID: 29228154 PMCID: PMC5803773 DOI: 10.1093/biolre/iox163] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/30/2017] [Indexed: 12/11/2022] Open
Abstract
Preterm birth affects 1 out of every 10 infants in the United States, resulting in substantial neonatal morbidity and mortality. Currently, there are few predictive markers and few treatment options to prevent preterm birth. A healthy, functioning placenta is essential to positive pregnancy outcomes. Previous studies have suggested that placental pathology may play a role in preterm birth etiology. Therefore, we tested the hypothesis that preterm placentae may exhibit unique transcriptomic signatures compared to term samples reflective of their abnormal biology leading to this adverse outcome. We aggregated publicly available placental villous microarray data to generate a preterm and term sample dataset (n = 133, 55 preterm placentae and 78 normal term placentae). We identified differentially expressed genes using the linear regression for microarray (LIMMA) package and identified perturbations in known biological networks using Differential Rank Conservation (DIRAC). We identified 129 significantly differentially expressed genes between term and preterm placenta with 96 genes upregulated and 33 genes downregulated (P-value <0.05). Significant changes in gene expression in molecular networks related to Tumor Protein 53 and phosphatidylinositol signaling were identified using DIRAC. We have aggregated a uniformly normalized transcriptomic dataset and have identified novel and established genes and pathways associated with developmental regulation of the placenta and potential preterm birth pathology. These analyses provide a community resource to integrate with other high-dimensional datasets for additional insights in normal placental development and its disruption.
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Affiliation(s)
| | - Heather M Brockway
- Division of Human Genetics, Center for Prevention of Preterm Birth, Cincinnati Children's, Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Louis J Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Cincinnati Children's, Hospital Medical Center, Cincinnati, Ohio, USA
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32
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Hobel CJ, Dolan SM, Hindoyan NA, Zhong N, Menon R. History of the establishment of the Preterm Birth international collaborative (PREBIC). Placenta 2019; 79:3-20. [PMID: 31047707 DOI: 10.1016/j.placenta.2019.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/16/2019] [Accepted: 03/20/2019] [Indexed: 01/25/2023]
Abstract
INTRODUCTION The primary aim of PREBIC is to assess the underlying mechanisms and developing strategies for preterm birth (PTB) prevention. MATERIALS AND METHODS We used concept mapping and logic models to track goals. This paper reviews our progress over 13 years using working group activities, research developments, guest speakers, and publications. RESULTS Using interactions between genetics, environment, and behaviors we identified complex interactions between biological systems. PREBIC determined that epidemiology and biomarkers should be an initial focus. In 2005, we initiated presentations by young investigators, yearly satellite meetings, working groups including nutrition and inflammation, assessment of clinical trials, and accepted an invitation by the WHO to begin yearly meetings in Geneva. DISCUSSION PREBIC used epidemiology to identify PTB factors and complex pathways. Candidate genes are associated with the environment, behavior (stress), obesity, inflammation and insulin resistance. Epigenetic changes and production of proteins can be used as biomarkers to define risk. Subsequently, we found risk factors for PTB that were also associated with the risk of cardiovascular disease (CVD) of the mother. Tanz et al. (2017) found that a history of PTB is independently predictive of CVD later in life and suggested that a modest proportion of PTB-CVD association was accounted by CVD risk factors, many of which have been identified in this paper. CONCLUSION Our findings support a relationship between genes, environment, behaviors and risk of CVD in women. The next several years must assess which factors are modifiable early in life and before pregnancy to prevent PTB.
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Affiliation(s)
- Calvin J Hobel
- Departments of OB/GYN & Pediatrics, Cedars-Sinai Medical Center, 8635 West 3rd St. Suite 160W, Los Angeles, CA, 90048, USA; David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, 90095-1740, USA.
| | - Siobhan M Dolan
- Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine, 1695 Eastchester Road Suite 301, Bronx, NY, 10461, USA.
| | - Niree A Hindoyan
- Department of Medicine, Cedars-Sinai Medical Center, 8730 Alden Drive Room W215, Los Angeles, CA, 90048, USA.
| | - Nanbert Zhong
- Developmental Genetics Laboratory, Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY, 10314, USA.
| | - Ramkumar Menon
- Department of Obstetrics and Gynecology, Maternal-Fetal Medicine, Perinatal Research Division, University of Texas Medical Branch MRB 11.138, 301 University Blvd, Galveston, TX, 7755-1062, USA.
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Souza RT, Mayrink J, Leite DF, Costa ML, Calderon IM, Rocha EA, Vettorazzi J, Feitosa FE, Cecatti JG. Metabolomics applied to maternal and perinatal health: a review of new frontiers with a translation potential. Clinics (Sao Paulo) 2019; 74:e894. [PMID: 30916173 PMCID: PMC6438130 DOI: 10.6061/clinics/2019/e894] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/27/2018] [Indexed: 12/31/2022] Open
Abstract
The prediction or early diagnosis of maternal complications is challenging mostly because the main conditions, such as preeclampsia, preterm birth, fetal growth restriction, and gestational diabetes mellitus, are complex syndromes with multiple underlying mechanisms related to their occurrence. Limited advances in maternal and perinatal health in recent decades with respect to preventing these disorders have led to new approaches, and "omics" sciences have emerged as a potential field to be explored. Metabolomics is the study of a set of metabolites in a given sample and can represent the metabolic functioning of a cell, tissue or organism. Metabolomics has some advantages over genomics, transcriptomics, and proteomics, as metabolites are the final result of the interactions of genes, RNAs and proteins. Considering the recent "boom" in metabolomic studies and their importance in the research agenda, we here review the topic, explaining the rationale and theory of the metabolomic approach in different areas of maternal and perinatal health research for clinical practitioners. We also demonstrate the main exploratory studies of these maternal complications, commenting on their promising findings. The potential translational application of metabolomic studies, especially for the identification of predictive biomarkers, is supported by the current findings, although they require external validation in larger datasets and with alternative methodologies.
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Affiliation(s)
- Renato Teixeira Souza
- Departamento de Ginecologia e Obstetricia, Faculdade de Ciencias Medicas, Universidade Estadual de Campinas, Campinas, SP, BR
| | - Jussara Mayrink
- Departamento de Ginecologia e Obstetricia, Faculdade de Ciencias Medicas, Universidade Estadual de Campinas, Campinas, SP, BR
| | - Débora Farias Leite
- Departamento de Ginecologia e Obstetricia, Faculdade de Ciencias Medicas, Universidade Estadual de Campinas, Campinas, SP, BR
- Departamento Materno Infantil, Faculdade de Medicina, Universidade Federal de Pernambuco, Pernambuco, PE, BR
| | - Maria Laura Costa
- Departamento de Ginecologia e Obstetricia, Faculdade de Ciencias Medicas, Universidade Estadual de Campinas, Campinas, SP, BR
| | - Iracema Mattos Calderon
- Departamento de Ginecologia e Obstetricia, Faculdade de Medicina de Botucatu, Universidade Estadual de Sao Paulo (UNESP), Botucatu, SP, BR
| | - Edilberto Alves Rocha
- Departamento Materno Infantil, Faculdade de Medicina, Universidade Federal de Pernambuco, Pernambuco, PE, BR
| | - Janete Vettorazzi
- Departamento de Ginecologia e Obstetricia, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Rio Grande do Sul, RS, BR
| | - Francisco Edson Feitosa
- Departamento de Ginecologia e Obstetricia, Faculdade de Medicina, Universidade Federal do Ceara, Ceara, CE, BR
| | - José Guilherme Cecatti
- Departamento de Ginecologia e Obstetricia, Faculdade de Ciencias Medicas, Universidade Estadual de Campinas, Campinas, SP, BR
- Corresponding author. E-mail:
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Souza RT, Galvão RB, Leite DFB, Passini R, Baker P, Cecatti JG. Use of metabolomics for predicting spontaneous preterm birth in asymptomatic pregnant women: protocol for a systematic review and meta-analysis. BMJ Open 2019; 9:e026033. [PMID: 30837257 PMCID: PMC6429842 DOI: 10.1136/bmjopen-2018-026033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Preterm birth (PTB) is the leading cause of neonatal mortality and short- and long-term morbidity. The aetiology and pathophysiology of spontaneous PTB (sPTB) are still unclear, which makes the identification of reliable and accurate predictor markers more difficult, particularly for unscreened or asymptomatic women. Metabolomics biomarkers have been demonstrated to be potentially accurate biomarkers for many disorders with complex mechanisms such as PTB. Therefore, we aim to perform a systematic review of metabolomics markers associated with sPTB. Our research question is 'What is the performance of metabolomics for predicting spontaneous preterm birth in asymptomatic pregnant women?' METHODS AND ANALYSIS We will focus on studies assessing metabolomics techniques for predicting sPTB in asymptomatic pregnant women. We will conduct a comprehensive systematic review of the literature from the last 10 years. Only observational cohort and case-control studies will be included. Our search strategy will be carried out by two independent reviewers, who will scan title and abstract before carrying out a full review of the article. The scientific databases to be explored include PubMed, MedLine, ScieLo, EMBASE, LILACS, Web of Science, Scopus and others. ETHICS AND DISSEMINATION This systematic review protocol does not require ethical approval. We intend to disseminate our findings in scientific peer-reviewed journal, the Preterm SAMBA study open access website, specialists' conferences and to our funding agencies. PROSPERO REGISTRATION NUMBER CRD42018100172.
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Affiliation(s)
- Renato T Souza
- Obstetrics and Gynecology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Rafael Bessa Galvão
- Obstetrics and Gynecology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Debora Farias Batista Leite
- Department of Tocogynecology, Campinas' State University, Campinas, Brazil
- Department of Maternal and Infant Health, Universidade Federal de Pernambuco, Recife, Brazil
| | - Renato Passini
- Universidade Estadual de Campinas Faculdade de Ciencias Medicas, Campinas, Brazil
| | - Philip Baker
- University of Leicester, College of Medicine, Leicester, UK
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Amylidi-Mohr S, Mueller M. [Preterm Birth Screening: What Does Really Make Sense?]. PRAXIS 2019; 108:53-57. [PMID: 30621535 DOI: 10.1024/1661-8157/a003137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Preterm Birth Screening: What Does Really Make Sense? Abstract. Spontaneous preterm birth is a syndrome triggered by multiple mechanisms. In view of the pathophysiological heterogeneity of preterm birth, a single biomarker cannot show the required high negative and positive predictive values. From a clinical point of view, anamnesis, sonographic measurement of cervical length, and placental alpha-microglobulin-1 (PAMG-1) testing from cervico-vaginal secretion are established. Further prospective, large-scale longitudinal studies must validate the combined use of new biomarkers.
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Affiliation(s)
- Sofia Amylidi-Mohr
- 1 Geburtshilfe und Feto-Maternale Medizin, Universitätsklinik für Frauenheilkunde, Inselspital Bern
| | - Martin Mueller
- 1 Geburtshilfe und Feto-Maternale Medizin, Universitätsklinik für Frauenheilkunde, Inselspital Bern
- 2 Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, USA
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Hou Q, Jiang C, Huang Y, Ye J, Yang X. Is maternal serum relaxin associated with preterm delivery in Chinese pregnant women? A meta-analysis. J Matern Fetal Neonatal Med 2018; 32:3357-3366. [PMID: 29788816 DOI: 10.1080/14767058.2018.1463983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Objective: A meta-analysis was performed to study the relationship between serum relaxin and preterm delivery in women with singleton pregnancies without estrogen stimulation. Methods: Cohort and case-control studies were identified through searching databases (PubMed, Embase, Ovid, CBM, Wan fang, VIP, and CNKI). We carried out a continuous variable meta-analysis. The outcome was preterm delivery (gestation age <37 weeks). Results: Fifteen studies were included, involving 1607 women with a singleton pregnancy. The pooled standard mean deviation (SMD) of 15 studies was 0.559 (95%CI: 0.002-1.196) and the heterogeneity was 96.6%. To reduce the heterogeneity, we chose random effects model and made subgroup analysis according to gestational age at sample testing (<18 weeks and ≥18 weeks) and race of included pregnant women. The pooled SMD of gestational age at sample testing ≥18 weeks and Chinese were 1.19 (95%CI: 0.63-1.75) and 1.61 (95%CI: 0.82-2.41) and the heterogeneity values (measured by I2) were 93.5% and 76.5%, respectively. Conclusions: Elevated maternal serum relaxin of later than 18 weeks of gestational age is associated with singleton preterm birth in Chinese women. It might be an important information to prevent singleton preterm delivery in Chinese women. What's already known about this topic? Previous reports reveal that there is a relationship between elevated maternal serum relaxin and preterm birth. However, the included articles contained twin pregnancies and estrogen stimulation, which obviously resulted in higher relaxin concentrations. What does this study add?
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Affiliation(s)
- Qingzhi Hou
- a Department of Occupational Health and Environmental Health , School of Public Health of Guangxi Medical University , Nanning , China.,b Center for Genomic and Personalized Medicine , Guangxi Medical University , Nanning , China
| | - Chao Jiang
- a Department of Occupational Health and Environmental Health , School of Public Health of Guangxi Medical University , Nanning , China.,b Center for Genomic and Personalized Medicine , Guangxi Medical University , Nanning , China
| | - Yaling Huang
- a Department of Occupational Health and Environmental Health , School of Public Health of Guangxi Medical University , Nanning , China.,b Center for Genomic and Personalized Medicine , Guangxi Medical University , Nanning , China
| | - Juan Ye
- a Department of Occupational Health and Environmental Health , School of Public Health of Guangxi Medical University , Nanning , China.,b Center for Genomic and Personalized Medicine , Guangxi Medical University , Nanning , China
| | - Xiaobo Yang
- a Department of Occupational Health and Environmental Health , School of Public Health of Guangxi Medical University , Nanning , China.,b Center for Genomic and Personalized Medicine , Guangxi Medical University , Nanning , China
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Watson E, Reid G. Metabolomics as a clinical testing method for the diagnosis of vaginal dysbiosis. Am J Reprod Immunol 2018; 80:e12979. [PMID: 29756665 DOI: 10.1111/aji.12979] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/18/2018] [Indexed: 12/19/2022] Open
Abstract
Microbes play an important role in vaginal health, with lactobacilli a particularly abundant species. When dysbiosis occurs, the tools to determine whether it is a condition such as bacterial vaginosis, and whether it warrants antibiotic treatment, are currently suboptimal. We propose that standardization and implementation of an affordable metabolomics-based diagnostic technique could reduce instances of false positives, stress associated with misdiagnosis, and potentially save time and money. Basing diagnosis on the detection of pH elevated above 4.5 and specific polyamines could provide a better method to assist a physician determine whether treatment is warranted.
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Affiliation(s)
- Emiley Watson
- Department of Microbiology, Immunology, and Surgery, The University of Western Ontario, London, ON, Canada
| | - Gregor Reid
- Department of Microbiology, Immunology, and Surgery, The University of Western Ontario, London, ON, Canada.,Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, ON, Canada
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Łopucki M, Wawrzykowski J, Gęca T, Miturski A, Franczyk M, Kankofer M. Preliminary analysis of the protein profile in saliva during physiological term and preterm delivery. Mol Med Rep 2018; 17:8253-8259. [PMID: 29693144 PMCID: PMC5983998 DOI: 10.3892/mmr.2018.8909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/01/2018] [Indexed: 11/06/2022] Open
Abstract
From a clinical point of view, easily obtainable and useful markers of a particular pathological status are required for appropriate diagnosis and treatment. Analysis of the proteomic profile of saliva may allow for the selection of potential marker of preterm delivery in humans. Saliva samples were collected from 12 patients diagnosed with threatened preterm delivery and 10 controls with uncomplicated pregnancies at the same gestational age. Samples were analysed using 2D electrophoresis. Based on statistical analysis, spots of interest were selected and collected from gels. Subsequently, spots were decoloured and proteins were identified by mass spectrometry using the matrix assisted laser desorption ionization-time of flight technique. The results of identification were compared with the Swiss-Prot database. A total of 1,393 spots were detected in the present study with 59 significantly different between control and preterm samples. Increased intensity of staining of 32 spots was observed in the premature delivery group compared with control patients and 27 spots were stained more intensely in the control group compared with the premature delivery group. A total of nine spots, which were significantly different between examined samples were identified and three of them exhibited increased intensity of staining in premature delivery group compared with controls, including dedicator of cytokinesis protein 1, metallothionein-2, guanylyl cyclase-activating protein 1. The six remaining spots included, epithelial-stromal interaction protein 1, serum albumin, tyrosine-tRNA ligase, cytoplasmic, protein chibby homolog 3, leukemia inhibitory factor receptor and adenosylhomocysteinase 3, and exhibited increased intensity of staining in healthy controls compared with premature delivery group. Further studies with an increased number of patients and identification of the complete protein profile are required to confirm the results of the present study and applicability of saliva as a source of disease biomarkers.
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Affiliation(s)
- Maciej Łopucki
- Department of Gynaecological Oncology and Gynaecology, Medical University of Lublin, 20‑081 Lublin, Poland
| | - Jacek Wawrzykowski
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20‑033 Lublin, Poland
| | - Tomasz Gęca
- Department of Obstetrics and Pathology of Pregnancy, Medical University of Lublin, 20‑081 Lublin, Poland
| | - Andrzej Miturski
- Department of Obstetrics and Pathology of Pregnancy, Medical University of Lublin, 20‑081 Lublin, Poland
| | - Monika Franczyk
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20‑033 Lublin, Poland
| | - Marta Kankofer
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20‑033 Lublin, Poland
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Optimising the collection of female genital tract fluid for cytokine analysis in pregnant women. J Immunol Methods 2018; 458:15-20. [PMID: 29625077 PMCID: PMC5981004 DOI: 10.1016/j.jim.2018.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/19/2018] [Accepted: 03/28/2018] [Indexed: 02/08/2023]
Abstract
Introduction To better understand the immunology of pregnancy, study of female genital tract fluid (FGF) is desirable. However the optimum method of collection of FGF in pregnant women for immunological methods, specifically cytokine measurement, is unknown. Methods A prospective study of HIV-uninfected pregnant women comparing two methods of FGF collection: polyvinyl acetal sponge collection of cervical fluid (CF) and menstrual cup collection of cervicovaginal fluid (CVF). Samples were collected at 3 time points across the second and third trimesters: 14–21, 22–25 and 26–31 weeks. Multiplex chemi-luminescent assays were used to measure: IFN-γ, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-13 and TNF-α. Optimal methodology for cytokine normalisation (sample weight, volume and total protein) was explored. Results All cytokines were measurable in both fluid types. IL-1β, IL-8 and IL-6 were detected at the highest concentrations (ranking order CF > CVF > plasma). CVF collection was simpler, provided the largest volume of sample (median 0.5 g) with the potential for undiluted usage, and allowed for self-insertion. CF cytokine concentrations were intrinsically associated with sample weight and protein concentration however CVF cytokines were independent of these. Conclusion Both methods of collection are robust for measurement of FGF cytokines during pregnancy. We recommend CVF collection using a menstrual cup as a viable option in pregnant women for high dimensional biological techniques. PVA sponges and MCs are robust methods for measuring FGF cytokines in pregnancy. MCs enable collection of large undiluted CVF volumes for high dimensional assays. CVF (not CF) cytokine concentrations are largely independent of sample weight or protein. Self-insertion and short collection time of MCs is an attractive option to women. Cytokine concentrations are higher in sponge samples reflecting the CF immune site.
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Paquette AG, Shynlova O, Kibschull M, Price ND, Lye SJ. Comparative analysis of gene expression in maternal peripheral blood and monocytes during spontaneous preterm labor. Am J Obstet Gynecol 2018; 218:345.e1-345.e30. [PMID: 29305255 DOI: 10.1016/j.ajog.2017.12.234] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 12/07/2017] [Accepted: 12/27/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Preterm birth is the leading cause of newborn death worldwide, and is associated with significant cognitive and physiological challenges in later life. There is a pressing need to define the mechanisms that initiate spontaneous preterm labor, and for development of novel clinical biomarkers to identify high-risk pregnancies. Most preterm birth studies utilize fetal tissues, and there is limited understanding of the transcriptional changes that occur in mothers undergoing spontaneous preterm labor. Earlier work revealed that a specific population of maternal peripheral leukocytes (macrophages/monocytes) play an active role in the initiation of labor. Thus, we hypothesized that there are dynamic gene expression changes in maternal blood leukocytes during preterm labor. OBJECTIVE Using next-generation sequencing we aim to characterize the transcriptome in whole blood leukocytes and peripheral monocytes of women undergoing spontaneous preterm labor compared to healthy pregnant women who subsequently delivered at full term. STUDY DESIGN RNA sequencing was performed in both whole blood and peripheral monocytes from women who underwent preterm labor (24-34 weeks of gestation, N = 20) matched for gestational age to healthy pregnant controls (N = 30). All participants were a part of the Ontario Birth Study cohort (Toronto, Ontario, Canada). RESULTS We identified significant differences in expression of 262 genes in peripheral monocytes and 184 genes in whole blood of women who were in active spontaneous preterm labor compared to pregnant women of the same gestational age not undergoing labor, with 43 of these genes differentially expressed in both whole blood and peripheral monocytes. ADAMTS2 expression was significantly increased in women actively undergoing spontaneous preterm labor, which we validated through digital droplet reverse transcriptase polymerase chain reaction. Intriguingly, we have also identified a number of gene sets including signaling by stem cell factor-KIT, nucleotide metabolism, and trans-Golgi network vesicle budding, which exhibited changes in relative gene expression that was predictive of preterm labor status in both maternal whole blood and peripheral monocytes. CONCLUSION This study is the first to investigate changes in both whole blood leukocytes and peripheral monocytes of women actively undergoing spontaneous preterm labor through robust transcript measurements from RNA sequencing. Our unique study design overcame confounding based on gestational age by collecting blood samples from women matched by gestational age, allowing us to study transcriptomic changes directly related to the active preterm parturition. We performed RNA profiling using whole genome sequencing, which is highly sensitive and allowed us to identify subtle changes in specific genes. ADAMTS2 expression emerged as a marker of prematurity within peripheral blood leukocytes, an accessible tissue that plays a functional role in signaling during the onset of labor. We identified changes in relative gene expression in a number of gene sets related to signaling in monocytes and whole blood of women undergoing spontaneous preterm labor compared to controls. These genes and pathways may help identify potential targets for the development of novel drugs for preterm birth prevention.
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Rattray NJW, Deziel NC, Wallach JD, Khan SA, Vasiliou V, Ioannidis JPA, Johnson CH. Beyond genomics: understanding exposotypes through metabolomics. Hum Genomics 2018; 12:4. [PMID: 29373992 PMCID: PMC5787293 DOI: 10.1186/s40246-018-0134-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/11/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Over the past 20 years, advances in genomic technology have enabled unparalleled access to the information contained within the human genome. However, the multiple genetic variants associated with various diseases typically account for only a small fraction of the disease risk. This may be due to the multifactorial nature of disease mechanisms, the strong impact of the environment, and the complexity of gene-environment interactions. Metabolomics is the quantification of small molecules produced by metabolic processes within a biological sample. Metabolomics datasets contain a wealth of information that reflect the disease state and are consequent to both genetic variation and environment. Thus, metabolomics is being widely adopted for epidemiologic research to identify disease risk traits. In this review, we discuss the evolution and challenges of metabolomics in epidemiologic research, particularly for assessing environmental exposures and providing insights into gene-environment interactions, and mechanism of biological impact. MAIN TEXT Metabolomics can be used to measure the complex global modulating effect that an exposure event has on an individual phenotype. Combining information derived from all levels of protein synthesis and subsequent enzymatic action on metabolite production can reveal the individual exposotype. We discuss some of the methodological and statistical challenges in dealing with this type of high-dimensional data, such as the impact of study design, analytical biases, and biological variance. We show examples of disease risk inference from metabolic traits using metabolome-wide association studies. We also evaluate how these studies may drive precision medicine approaches, and pharmacogenomics, which have up to now been inefficient. Finally, we discuss how to promote transparency and open science to improve reproducibility and credibility in metabolomics. CONCLUSIONS Comparison of exposotypes at the human population level may help understanding how environmental exposures affect biology at the systems level to determine cause, effect, and susceptibilities. Juxtaposition and integration of genomics and metabolomics information may offer additional insights. Clinical utility of this information for single individuals and populations has yet to be routinely demonstrated, but hopefully, recent advances to improve the robustness of large-scale metabolomics will facilitate clinical translation.
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Affiliation(s)
- Nicholas J. W. Rattray
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA
| | - Nicole C. Deziel
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA
| | - Joshua D. Wallach
- Collaboration for Research Integrity and Transparency (CRIT), Yale Law School, New Haven, CT USA
- Center for Outcomes Research and Evaluation (CORE), Yale-New Haven Health System, New Haven, CT USA
| | - Sajid A. Khan
- Department of Surgery, Section of Surgical Oncology, Yale University School of Medicine, New Haven, CT USA
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT USA
| | - John P. A. Ioannidis
- Stanford Prevention Research Center, Department of Medicine, Stanford University, Stanford, CA USA
- Department of Health Research and Policy, Stanford University, Stanford, CA USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA USA
- Department of Statistics, Stanford University, Stanford, CA USA
- Meta-Research Innovation Center at Stanford, Stanford University, Stanford, CA USA
| | - Caroline H. Johnson
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT USA
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Quinney SK, Gullapelli R, Haas DM. Translational Systems Pharmacology Studies in Pregnant Women. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017; 7:69-81. [PMID: 29239132 PMCID: PMC5824114 DOI: 10.1002/psp4.12269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 12/26/2022]
Abstract
Pregnancy involves rapid physiological adaptation and complex interplay between mother and fetus. New analytic technologies provide large amounts of genomic, proteomic, and metabolomics data. The integration of these data through bioinformatics, statistical, and systems pharmacology techniques can improve our understanding of the mechanisms of normal maternal physiologic changes and fetal development. New insights into the mechanisms of pregnancy‐related disorders, such as preterm birth (PTB), may lead to the development of new therapeutic interventions and novel biomarkers.
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Affiliation(s)
- Sara K Quinney
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Rakesh Gullapelli
- School of Informatics and Computing, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - David M Haas
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Urinary metabolomic analysis to identify preterm neonates exposed to histological chorioamnionitis: A pilot study. PLoS One 2017; 12:e0189120. [PMID: 29211784 PMCID: PMC5718427 DOI: 10.1371/journal.pone.0189120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/20/2017] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVE Chorioamnionitis is a leading cause of preterm birth worldwide, with higher incidence at lower gestational ages. An early and reliable diagnosis of histological chorioamnionitis (HCA) in preterm infants may be helpful in guiding postnatal management, especially the administration of prophylactic antibiotics to prevent early-onset sepsis. The main aim of this study was to investigate metabolomic analysis of urines collected in the first 24 hours of life as diagnostic tool of HCA. METHODS Gestational age-, birth weight-, delivery mode- and sex- matched (1:2) preterm neonates (< 35 weeks' gestation) born to mothers with or without HCA were enrolled from an observational study. Gas chromatography-mass spectrometry (GC-MS)-based metabolomic analysis was performed on urine samples non-invasively collected in the first 24 hours of life. Univariate analysis, partial least square discriminant analysis (PLS-DA) and its associated variable importance in projection (VIP) score were performed. The most affected metabolic pathways were examined by Metabolite Sets Enrichment Analysis (MSEA). RESULTS Fifteen cases (mean GA 30.2 ± 3.8 weeks, mean BW 1415 ± 471.9 grams) and 30 controls (mean GA 30.2 ± 2.9 weeks, mean BW 1426 ± 569.8 grams) were enrolled. Following univariate analysis, 29 metabolites had a significantly different concentration between cases and controls. The supervised PLS-DA model confirmed a separation between the two groups. Only gluconic acid, an oxidation product of glucose, was higher in cases than in controls. All other VIP metabolites were more abundant in the control group. Glutamate metabolism, mitochondrial electron transport chain, citric acid cycle, galactose metabolism, and fructose and mannose degradation metabolism were the most significantly altered pathways (P < 0.01). CONCLUSIONS For the first time, urinary metabolomics was able to discriminate neonates born to mothers with and without HCA. The identification of specifically altered metabolic pathways may be helpful in understanding metabolic derangement following chorioamnionitis.
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Probing for Sparse and Fast Variable Selection with Model-Based Boosting. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2017; 2017:1421409. [PMID: 28831289 PMCID: PMC5555005 DOI: 10.1155/2017/1421409] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/13/2017] [Indexed: 11/17/2022]
Abstract
We present a new variable selection method based on model-based gradient boosting and randomly permuted variables. Model-based boosting is a tool to fit a statistical model while performing variable selection at the same time. A drawback of the fitting lies in the need of multiple model fits on slightly altered data (e.g., cross-validation or bootstrap) to find the optimal number of boosting iterations and prevent overfitting. In our proposed approach, we augment the data set with randomly permuted versions of the true variables, so-called shadow variables, and stop the stepwise fitting as soon as such a variable would be added to the model. This allows variable selection in a single fit of the model without requiring further parameter tuning. We show that our probing approach can compete with state-of-the-art selection methods like stability selection in a high-dimensional classification benchmark and apply it on three gene expression data sets.
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Erez O, Romero R, Maymon E, Chaemsaithong P, Done B, Pacora P, Panaitescu B, Chaiworapongsa T, Hassan SS, Tarca AL. The prediction of late-onset preeclampsia: Results from a longitudinal proteomics study. PLoS One 2017; 12:e0181468. [PMID: 28738067 PMCID: PMC5524331 DOI: 10.1371/journal.pone.0181468] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/30/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Late-onset preeclampsia is the most prevalent phenotype of this syndrome; nevertheless, only a few biomarkers for its early diagnosis have been reported. We sought to correct this deficiency using a high through-put proteomic platform. METHODS A case-control longitudinal study was conducted, including 90 patients with normal pregnancies and 76 patients with late-onset preeclampsia (diagnosed at ≥34 weeks of gestation). Maternal plasma samples were collected throughout gestation (normal pregnancy: 2-6 samples per patient, median of 2; late-onset preeclampsia: 2-6, median of 5). The abundance of 1,125 proteins was measured using an aptamers-based proteomics technique. Protein abundance in normal pregnancies was modeled using linear mixed-effects models to estimate mean abundance as a function of gestational age. Data was then expressed as multiples of-the-mean (MoM) values in normal pregnancies. Multi-marker prediction models were built using data from one of five gestational age intervals (8-16, 16.1-22, 22.1-28, 28.1-32, 32.1-36 weeks of gestation). The predictive performance of the best combination of proteins was compared to placental growth factor (PIGF) using bootstrap. RESULTS 1) At 8-16 weeks of gestation, the best prediction model included only one protein, matrix metalloproteinase 7 (MMP-7), that had a sensitivity of 69% at a false positive rate (FPR) of 20% (AUC = 0.76); 2) at 16.1-22 weeks of gestation, MMP-7 was the single best predictor of late-onset preeclampsia with a sensitivity of 70% at a FPR of 20% (AUC = 0.82); 3) after 22 weeks of gestation, PlGF was the best predictor of late-onset preeclampsia, identifying 1/3 to 1/2 of the patients destined to develop this syndrome (FPR = 20%); 4) 36 proteins were associated with late-onset preeclampsia in at least one interval of gestation (after adjustment for covariates); 5) several biological processes, such as positive regulation of vascular endothelial growth factor receptor signaling pathway, were perturbed; and 6) from 22.1 weeks of gestation onward, the set of proteins most predictive of severe preeclampsia was different from the set most predictive of the mild form of this syndrome. CONCLUSIONS Elevated MMP-7 early in gestation (8-22 weeks) and low PlGF later in gestation (after 22 weeks) are the strongest predictors for the subsequent development of late-onset preeclampsia, suggesting that the optimal identification of patients at risk may involve a two-step diagnostic process.
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Affiliation(s)
- Offer Erez
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, 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, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Maternity Department “D” and Obstetrical Day Care Center, Division of Obstetrics and Gynecology, Soroka University Medical Center, School of Medicine, Faculty of Heath Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Roberto Romero
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, 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, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, United States of America
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
- * E-mail: (RR); (ALT)
| | - Eli Maymon
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, 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, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Piya Chaemsaithong
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, 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, Bethesda, Maryland, and Detroit, Michigan, United States of America
| | - Bogdan Done
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, 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, Bethesda, Maryland, and Detroit, Michigan, United States of America
| | - Percy Pacora
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, 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, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Bogdan Panaitescu
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, 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, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, 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, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Sonia S. Hassan
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, 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, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Adi L. Tarca
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, 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, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Computer Science, Wayne State University College of Engineering, Detroit, Michigan, United States of America
- * E-mail: (RR); (ALT)
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Romero R, Erez O, Maymon E, Chaemsaithong P, Xu Z, Pacora P, Chaiworapongsa T, Done B, Hassan SS, Tarca AL. The maternal plasma proteome changes as a function of gestational age in normal pregnancy: a longitudinal study. Am J Obstet Gynecol 2017; 217:67.e1-67.e21. [PMID: 28263753 PMCID: PMC5813489 DOI: 10.1016/j.ajog.2017.02.037] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/10/2017] [Accepted: 02/23/2017] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Pregnancy is accompanied by dramatic physiological changes in maternal plasma proteins. Characterization of the maternal plasma proteome in normal pregnancy is an essential step for understanding changes to predict pregnancy outcome. The objective of this study was to describe maternal plasma proteins that change in abundance with advancing gestational age and determine biological processes that are perturbed in normal pregnancy. STUDY DESIGN A longitudinal study included 43 normal pregnancies that had a term delivery of an infant who was appropriate for gestational age without maternal or neonatal complications. For each pregnancy, 3 to 6 maternal plasma samples (median, 5) were profiled to measure the abundance of 1125 proteins using multiplex assays. Linear mixed-effects models with polynomial splines were used to model protein abundance as a function of gestational age, and the significance of the association was inferred via likelihood ratio tests. Proteins considered to be significantly changed were defined as having the following: (1) >1.5-fold change between 8 and 40 weeks of gestation; and (2) a false discovery rate-adjusted value of P < .1. Gene ontology enrichment analysis was used to identify biological processes overrepresented among the proteins that changed with advancing gestation. RESULTS The following results were found: (1) Ten percent (112 of 1125) of the profiled proteins changed in abundance as a function of gestational age; (2) of the 1125 proteins analyzed, glypican-3, sialic acid-binding immunoglobulin-type lectin-6, placental growth factor, C-C motif-28, carbonic anhydrase 6, prolactin, interleukin-1 receptor 4, dual-specificity mitogen-activated protein kinase 4, and pregnancy-associated plasma protein-A had more than a 5-fold change in abundance across gestation (these 9 proteins are known to be involved in a wide range of both physiological and pathological processes, such as growth regulation, embryogenesis, angiogenesis immunoregulation, inflammation etc); and (3) biological processes associated with protein changes in normal pregnancy included defense response, defense response to bacteria, proteolysis, and leukocyte migration (false discovery rate, 10%). CONCLUSION The plasma proteome of normal pregnancy demonstrates dramatic changes in both the magnitude of changes and the fraction of the proteins involved. Such information is important to understand the physiology of pregnancy and the development of biomarkers to differentiate normal vs abnormal pregnancy and determine the response to interventions.
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Affiliation(s)
- Roberto Romero
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI.
| | - Offer Erez
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Eli Maymon
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Piya Chaemsaithong
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Zhonghui Xu
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI
| | - Percy Pacora
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Bogdan Done
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI
| | - Sonia S Hassan
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Adi L Tarca
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI.
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El-Azzamy H, Balogh A, Romero R, Xu Y, LaJeunesse C, Plazyo O, Xu Z, Price TG, Dong Z, Tarca AL, Papp Z, Hassan SS, Chaiworapongsa T, Kim CJ, Gomez-Lopez N, Than NG. Characteristic Changes in Decidual Gene Expression Signature in Spontaneous Term Parturition. J Pathol Transl Med 2017; 51:264-283. [PMID: 28226203 PMCID: PMC5445200 DOI: 10.4132/jptm.2016.12.20] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/03/2016] [Accepted: 12/20/2016] [Indexed: 11/29/2022] Open
Abstract
Background The decidua has been implicated in the “terminal pathway” of human term parturition, which is characterized by the activation of pro-inflammatory pathways in gestational tissues. However, the transcriptomic changes in the decidua leading to terminal pathway activation have not been systematically explored. This study aimed to compare the decidual expression of developmental signaling and inflammation-related genes before and after spontaneous term labor in order to reveal their involvement in this process. Methods Chorioamniotic membranes were obtained from normal pregnant women who delivered at term with spontaneous labor (TIL, n = 14) or without labor (TNL, n = 15). Decidual cells were isolated from snap-frozen chorioamniotic membranes with laser microdissection. The expression of 46 genes involved in decidual development, sex steroid and prostaglandin signaling, as well as pro- and anti-inflammatory pathways, was analyzed using high-throughput quantitative real-time polymerase chain reaction (qRT-PCR). Chorioamniotic membrane sections were immunostained and then semi-quantified for five proteins, and immunoassays for three chemokines were performed on maternal plasma samples. Results The genes with the highest expression in the decidua at term gestation included insulin-like growth factor-binding protein 1 (IGFBP1), galectin-1 (LGALS1), and progestogen-associated endometrial protein (PAEP); the expression of estrogen receptor 1 (ESR1), homeobox A11 (HOXA11), interleukin 1β (IL1B), IL8, progesterone receptor membrane component 2 (PGRMC2), and prostaglandin E synthase (PTGES) was higher in TIL than in TNL cases; the expression of chemokine C-C motif ligand 2 (CCL2), CCL5, LGALS1, LGALS3, and PAEP was lower in TIL than in TNL cases; immunostaining confirmed qRT-PCR data for IL-8, CCL2, galectin-1, galectin-3, and PAEP; and no correlations between the decidual gene expression and the maternal plasma protein concentrations of CCL2, CCL5, and IL-8 were found. Conclusions Our data suggests that with the initiation of parturition, the decidual expression of anti-inflammatory mediators decreases, while the expression of pro-inflammatory mediators and steroid receptors increases. This shift may affect downstream signaling pathways that can lead to parturition.
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Affiliation(s)
- Haidy El-Azzamy
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA
| | - Andrea Balogh
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA.,Department of Immunology, Eotvos Lorand University, Budapest, Hungary
| | - Roberto Romero
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and 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
| | - Yi Xu
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA
| | | | - Olesya Plazyo
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA
| | - Zhonghui Xu
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA
| | - Theodore G Price
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA
| | - Zhong Dong
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA
| | - Adi L Tarca
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University, School of Medicine, Detroit, MI, USA
| | - Zoltan Papp
- Maternity Private Department, Kutvolgyi Clinical Block, Semmelweis University, Budapest, Hungary
| | - Sonia S Hassan
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University, School of Medicine, Detroit, MI, USA
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University, School of Medicine, Detroit, MI, USA
| | - Chong Jai Kim
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA.,Department of Pathology, Wayne State University, School of Medicine, Detroit, MI, USA.,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University, School of Medicine, Detroit, MI, USA
| | - Nandor Gabor Than
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University, School of Medicine, Detroit, MI, USA.,Maternity Private Department, Kutvolgyi Clinical Block, Semmelweis University, Budapest, Hungary.,Systems Biology of Reproduction Lendulet 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
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Renal injury in neonates: use of "omics" for developing precision medicine in neonatology. Pediatr Res 2017; 81:271-276. [PMID: 27723726 DOI: 10.1038/pr.2016.206] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/05/2016] [Indexed: 12/18/2022]
Abstract
Preterm birth is associated with increased risks of morbidity and mortality along with increased healthcare costs. Advances in medicine have enhanced survival for preterm infants but the overall incidence of major morbidities has changed very little. Abnormal renal development is an important consequence of premature birth. Acute kidney injury (AKI) in the neonatal period is multifactorial and may increase lifetime risk of chronic kidney disease.Traditional biomarkers in newborns suffer from considerable confounders, limiting their use for early identification of AKI. There is a need to develop novel biomarkers that can identify, in real time, the evolution of renal dysfunction in an early diagnostic, monitoring and prognostic fashion. Use of "omics", particularly metabolomics, may provide valuable information regarding functional pathways underlying AKI and prediction of clinical outcomes.The emerging knowledge generated by the application of "omics" (genomics, proteomics, metabolomics) in neonatology provides new insights that can help to identify markers of early diagnosis, disease progression, and identify new therapeutic targets. Additionally, omics will have major implications in the field of personalized healthcare in the future. Here, we will review the current knowledge of different omics technologies in neonatal-perinatal medicine including biomarker discovery, defining as yet unrecognized biologic therapeutic targets, and linking of omics to relevant standard indices and long-term outcomes.
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Lv H, Jiang F, Guan D, Lu C, Guo B, Chan C, Peng S, Liu B, Guo W, Zhu H, Xu X, Lu A, Zhang G. Metabolomics and Its Application in the Development of Discovering Biomarkers for Osteoporosis Research. Int J Mol Sci 2016; 17:E2018. [PMID: 27918446 PMCID: PMC5187818 DOI: 10.3390/ijms17122018] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/17/2016] [Accepted: 11/28/2016] [Indexed: 12/30/2022] Open
Abstract
Osteoporosis is a progressive skeletal disorder characterized by low bone mass and increased risk of fracture in later life. The incidence and costs associated with treating osteoporosis cause heavy socio-economic burden. Currently, the diagnosis of osteoporosis mainly depends on bone mineral density and bone turnover markers. However, these indexes are not sensitive and accurate enough to reflect the osteoporosis progression. Metabolomics offers the potential for a holistic approach for clinical diagnoses and treatment, as well as understanding of the pathological mechanism of osteoporosis. In this review, we firstly describe the study subjects of osteoporosis and bio-sample preparation procedures for different analytic purposes, followed by illustrating the biomarkers with potentially predictive, diagnosis and pharmaceutical values when applied in osteoporosis research. Then, we summarize the published metabolic pathways related to osteoporosis. Furthermore, we discuss the importance of chronological data and combination of multi-omics in fully understanding osteoporosis. The application of metabolomics in osteoporosis could provide researchers the opportunity to gain new insight into the metabolic profiling and pathophysiological mechanisms. However, there is still much to be done to validate the potential biomarkers responsible for the progression of osteoporosis and there are still many details needed to be further elucidated.
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Affiliation(s)
- Huanhuan Lv
- Institute for Advancing Translational Medicine in Bone & Joint Disease, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226133, China.
| | - Feng Jiang
- Institute for Advancing Translational Medicine in Bone & Joint Disease, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226133, China.
| | - Daogang Guan
- Institute for Advancing Translational Medicine in Bone & Joint Disease, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Cheng Lu
- Institute for Advancing Translational Medicine in Bone & Joint Disease, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Baosheng Guo
- Institute for Advancing Translational Medicine in Bone & Joint Disease, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Chileung Chan
- Institute for Advancing Translational Medicine in Bone & Joint Disease, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Songlin Peng
- Deparment of Spine Surgery, Shenzheng People's Hospital, Shenzheng 518020, China.
| | - Baoqin Liu
- Zhengzhou Hospital of Traditional Chinese Medicine, Zhengzhou 450007, China.
| | - Wenwei Guo
- Zhengzhou Hospital of Traditional Chinese Medicine, Zhengzhou 450007, China.
| | - Hailong Zhu
- Institute for Advancing Translational Medicine in Bone & Joint Disease, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Xuegong Xu
- Zhengzhou Hospital of Traditional Chinese Medicine, Zhengzhou 450007, China.
| | - Aiping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Disease, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Guanghua Integrative Medicine Hospital/Shanghai University of Traditional Chinese Medicine, Shanghai 200052, China.
| | - Ge Zhang
- Institute for Advancing Translational Medicine in Bone & Joint Disease, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
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Wu PY, Cheng CW, Kaddi CD, Venugopalan J, Hoffman R, Wang MD. -Omic and Electronic Health Record Big Data Analytics for Precision Medicine. IEEE Trans Biomed Eng 2016; 64:263-273. [PMID: 27740470 DOI: 10.1109/tbme.2016.2573285] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Rapid advances of high-throughput technologies and wide adoption of electronic health records (EHRs) have led to fast accumulation of -omic and EHR data. These voluminous complex data contain abundant information for precision medicine, and big data analytics can extract such knowledge to improve the quality of healthcare. METHODS In this paper, we present -omic and EHR data characteristics, associated challenges, and data analytics including data preprocessing, mining, and modeling. RESULTS To demonstrate how big data analytics enables precision medicine, we provide two case studies, including identifying disease biomarkers from multi-omic data and incorporating -omic information into EHR. CONCLUSION Big data analytics is able to address -omic and EHR data challenges for paradigm shift toward precision medicine. SIGNIFICANCE Big data analytics makes sense of -omic and EHR data to improve healthcare outcome. It has long lasting societal impact.
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