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Papaefthimiou M, Kontou PI, Bagos PG, Braliou GG. Integration of Antioxidant Activity Assays Data of Stevia Leaf Extracts: A Systematic Review and Meta-Analysis. Antioxidants (Basel) 2024; 13:692. [PMID: 38929131 PMCID: PMC11201069 DOI: 10.3390/antiox13060692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Stevia rebaudiana Bertoni, a no-calorie natural sweetener, contains a plethora of polyphenols that exert antioxidant properties with potential medicinal significance. Due to the variety of functional groups, polyphenols exhibit varying solubility depending on the nature of the extraction solvents (water, organic, or their mixtures, defined further on as hydroalcoholic extracts). In the present study, we performed a systematic review, following PRISMA guidelines, and meta-analysis, synthesizing all available data from 45 articles encompassing 250 different studies. Our results showed that the total phenolic content (TPC) of hydroalcoholic and aqueous extracts presents higher values (64.77 and 63.73 mg GAE/g) compared to organic extracts (33.39). Total flavonoid content (TFC) was also higher in aqueous and hydroalcoholic extracts; meta-regression analysis revealed that outcomes in different measuring units (mg QE/g, mg CE/g, and mg RUE/g) do not present statistically significant differences and can be synthesized in meta-analysis. Using meta-regression analysis, we showed that outcomes from the chemical-based ABTS, FRAP, and ORAC antioxidant assays for the same extract type can be combined in meta-analysis because they do not differ statistically significantly. Meta-analysis of ABTS, FRAP, and ORAC assays outcomes revealed that the antioxidant activity profile of various extract types follows that of their phenolic and flavonoid content. Using regression meta-analysis, we also presented that outcomes from SOD, CAT, and POX enzymatic antioxidant assays are independent of the assay type (p-value = 0.905) and can be combined. Our study constitutes the first effort to quantitatively and statistically synthesize the research results of individual studies using all methods measuring the antioxidant activity of stevia leaf extracts. Our results, in light of evidence-based practice, uncover the need for a broadly accepted, unified, methodological strategy to perform antioxidant tests, and offer documentation that the use of ethanol:water 1:1 mixtures or pure water can more efficiently extract stevia antioxidant compounds.
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Affiliation(s)
- Maria Papaefthimiou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (M.P.); (P.G.B.)
| | | | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (M.P.); (P.G.B.)
| | - Georgia G. Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (M.P.); (P.G.B.)
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Wang X, Wei Y, Wei F, Kuang H. Regulatory mechanism and research progress of ferroptosis in obstetrical and gynecological diseases. Front Cell Dev Biol 2023; 11:1146971. [PMID: 37065851 PMCID: PMC10098117 DOI: 10.3389/fcell.2023.1146971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023] Open
Abstract
Ferroptosis is a novel type of regulated cell death driven by iron-dependent lipid peroxidation, which is distinguished from traditional types of programmed cell death, such as apoptosis, proptosis and necrosis et al. Impaired iron homeostasis, lipid peroxidation and antioxidants depletion are three hallmarks of ferroptosis. Over the past years, emerging studies support the notion that ferroptosis might be involved in the pathology of obstetrical and gynecological diseases, including preeclampsia (PE), endometriosis (EMs) and polycystic ovarian syndrome (PCOS). In the PE condition, the high sensitivity of trophoblasts towards ferroptosis has been found to potentially link to inflammation, suboptimal vascular remodeling and aberrant hemodynamics, which are three prominent pathophysiological features of PE. As for EMs, compromised ferroptosis of endometrial cells was associated with the formation ectopic lesions, whereas in the nearby lesions, the presence of ferroptosis was suggested to promote the progression of EMs, contributing to the relative clinical manifestations. Ferroptosis has been implicated a crucial role in the initiation of ovarian follicular atresia, which might help to manage ovulation in PCOS patients. Taken together, this review explored the basis of ferroptosis mechanisms and comprehensively summarized the latest discovery of roles of ferroptosis on PE, EMs and PCOS, gaining a deeper insight into the pathogenesis of these obstetrical and gynecological diseases and investigation of novel therapeutic interventions.
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Affiliation(s)
- Xinyue Wang
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, China
- Department of Clinical Medicine, School of Queen Mary, Nanchang University, Nanchang, China
| | - Yanchen Wei
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, China
- Department of Clinical Medicine, School of Queen Mary, Nanchang University, Nanchang, China
| | - Fangyi Wei
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, China
- Department of Clinical Medicine, School of Queen Mary, Nanchang University, Nanchang, China
| | - Haibin Kuang
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Reproductive Physiology and Pathology, Nanchang University, Nanchang, China
- *Correspondence: Haibin Kuang,
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Brockway HM, Wilson SL, Kallapur SG, Buhimschi CS, Muglia LJ, Jones HN. Characterization of methylation profiles in spontaneous preterm birth placental villous tissue. PLoS One 2023; 18:e0279991. [PMID: 36952446 PMCID: PMC10035933 DOI: 10.1371/journal.pone.0279991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Indexed: 03/25/2023] Open
Abstract
Preterm birth is a global public health crisis which results in significant neonatal and maternal mortality. Yet little is known regarding the molecular mechanisms of idiopathic spontaneous preterm birth, and we have few diagnostic markers for adequate assessment of placental development and function. Previous studies of placental pathology and our transcriptomics studies suggest a role for placental maturity in idiopathic spontaneous preterm birth. It is known that placental DNA methylation changes over gestation. We hypothesized that if placental hypermaturity is present in our samples, we would observe a unique idiopathic spontaneous preterm birth DNA methylation profile potentially driving the gene expression differences we previously identified in our placental samples. Our results indicate the idiopathic spontaneous preterm birth DNA methylation pattern mimics the term birth methylation pattern suggesting hypermaturity. Only seven significant differentially methylated regions fitting the idiopathic spontaneous preterm birth specific (relative to the controls) profile were identified, indicating unusually high similarity in DNA methylation between idiopathic spontaneous preterm birth and term birth samples. We identified an additional 1,718 significantly methylated regions in our gestational age matched controls where the idiopathic spontaneous preterm birth DNA methylation pattern mimics the term birth methylation pattern, again indicating a striking level of similarity between the idiopathic spontaneous preterm birth and term birth samples. Pathway analysis of these regions revealed differences in genes within the WNT and Cadherin signaling pathways, both of which are essential in placental development and maturation. Taken together, these data demonstrate that the idiopathic spontaneous preterm birth samples display a hypermature methylation signature than expected given their respective gestational age which likely impacts birth timing.
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Affiliation(s)
- Heather M. Brockway
- Department of Physiology and Functional Genomics, College of Medicine at the University of Florida, Gainesville, Florida, United States of America
| | - Samantha L. Wilson
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Suhas G. Kallapur
- Divisions of Neonatology and Developmental Biology, David Geffen School of Medicine at the University of California, UCLA Mattel Children’s Hospital, Los Angeles, California, United States of America
| | - Catalin S. Buhimschi
- Department of Obstetrics and Gynecology, The University of Illinois College of Medicine, Chicago, Illinois, United States of America
| | - Louis J. Muglia
- Burroughs Wellcome Fund, Research Triangle Park, North Carolina, United States of America
| | - Helen N. Jones
- Department of Physiology and Functional Genomics, College of Medicine at the University of Florida, Gainesville, Florida, United States of America
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Campbell KA, Colacino JA, Puttabyatappa M, Dou JF, Elkin ER, Hammoud SS, Domino SE, Dolinoy DC, Goodrich JM, Loch-Caruso R, Padmanabhan V, Bakulski KM. Placental cell type deconvolution reveals that cell proportions drive preeclampsia gene expression differences. Commun Biol 2023; 6:264. [PMID: 36914823 PMCID: PMC10011423 DOI: 10.1038/s42003-023-04623-6] [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: 09/09/2021] [Accepted: 02/22/2023] [Indexed: 03/14/2023] Open
Abstract
The placenta mediates adverse pregnancy outcomes, including preeclampsia, which is characterized by gestational hypertension and proteinuria. Placental cell type heterogeneity in preeclampsia is not well-understood and limits mechanistic interpretation of bulk gene expression measures. We generated single-cell RNA-sequencing samples for integration with existing data to create the largest deconvolution reference of 19 fetal and 8 maternal cell types from placental villous tissue (n = 9 biological replicates) at term (n = 40,494 cells). We deconvoluted eight published microarray case-control studies of preeclampsia (n = 173 controls, 157 cases). Preeclampsia was associated with excess extravillous trophoblasts and fewer mesenchymal and Hofbauer cells. Adjustment for cellular composition reduced preeclampsia-associated differentially expressed genes (log2 fold-change cutoff = 0.1, FDR < 0.05) from 1154 to 0, whereas downregulation of mitochondrial biogenesis, aerobic respiration, and ribosome biogenesis were robust to cell type adjustment, suggesting direct changes to these pathways. Cellular composition mediated a substantial proportion of the association between preeclampsia and FLT1 (37.8%, 95% CI [27.5%, 48.8%]), LEP (34.5%, 95% CI [26.0%, 44.9%]), and ENG (34.5%, 95% CI [25.0%, 45.3%]) overexpression. Our findings indicate substantial placental cellular heterogeneity in preeclampsia contributes to previously observed bulk gene expression differences. This deconvolution reference lays the groundwork for cellular heterogeneity-aware investigation into placental dysfunction and adverse birth outcomes.
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Affiliation(s)
- Kyle A Campbell
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Justin A Colacino
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - John F Dou
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Elana R Elkin
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Saher S Hammoud
- Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Steven E Domino
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Rita Loch-Caruso
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kelly M Bakulski
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
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Abstract
Pre-eclampsia is a life-threatening disease of pregnancy unique to humans and a leading cause of maternal and neonatal morbidity and mortality. Women who survive pre-eclampsia have reduced life expectancy, with increased risks of stroke, cardiovascular disease and diabetes, while babies from a pre-eclamptic pregnancy have increased risks of preterm birth, perinatal death and neurodevelopmental disability and cardiovascular and metabolic disease later in life. Pre-eclampsia is a complex multisystem disease, diagnosed by sudden-onset hypertension (>20 weeks of gestation) and at least one other associated complication, including proteinuria, maternal organ dysfunction or uteroplacental dysfunction. Pre-eclampsia is found only when a placenta is or was recently present and is classified as preterm (delivery <37 weeks of gestation), term (delivery ≥37 weeks of gestation) and postpartum pre-eclampsia. The maternal syndrome of pre-eclampsia is driven by a dysfunctional placenta, which releases factors into maternal blood causing systemic inflammation and widespread maternal endothelial dysfunction. Available treatments target maternal hypertension and seizures, but the only 'cure' for pre-eclampsia is delivery of the dysfunctional placenta and baby, often prematurely. Despite decades of research, the aetiology of pre-eclampsia, particularly of term and postpartum pre-eclampsia, remains poorly defined. Significant advances have been made in the prediction and prevention of preterm pre-eclampsia, which is predicted in early pregnancy through combined screening and is prevented with daily low-dose aspirin, starting before 16 weeks of gestation. By contrast, the prediction of term and postpartum pre-eclampsia is limited and there are no preventive treatments. Future research must investigate the pathogenesis of pre-eclampsia, in particular of term and postpartum pre-eclampsia, and evaluate new prognostic tests and treatments in adequately powered clinical trials.
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Reshetnikov EA, Stepanov VA, Serebrova VN, Bocharova AV, Trifonova EA, Ponomarenko IV, Reshetnikova YN, Efremova OA, Orlova VS, Batlutskaya IV, Sorokina IN, Churnosov MI. Genes TMEM136 and PPP1R12C Differentially Expressed in the Placenta Are Associated with Preeclampsia. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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7
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Abramova MY, Ponomarenko IV, Churnosov MI. The Polymorphic Locus rs167479 of the RGL3 Gene Is Associated with the Risk of Severe Preeclampsia. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542212002x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Czamara D, Cruceanu C, Lahti-Pulkkinen M, Dieckmann L, Ködel M, Sauer S, Rex-Haffner M, Sammallahti S, Kajantie E, Laivuori H, Lahti J, Räikkönen K, Binder EB. Genome-Wide Copy Number Variant and High-Throughput Transcriptomics Analyses of Placental Tissues Underscore Persisting Child Susceptibility in At-Risk Pregnancies Cleared in Standard Genetic Testing. Int J Mol Sci 2022; 23:ijms231911448. [PMID: 36232765 PMCID: PMC9569583 DOI: 10.3390/ijms231911448] [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: 08/09/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Several studies have shown that children from pregnancies with estimated first-trimester risk based on fetal nuchal translucency thickness and abnormal maternal serum pregnancy protein and hormone levels maintain a higher likelihood of adverse outcomes, even if initial testing for known genetic conditions is negative. We used the Finnish InTraUterine cohort (ITU), which is a comprehensively characterized perinatal cohort consisting of 943 mothers and their babies followed throughout pregnancy and 18 months postnatally, including mothers shortlisted for prenatal genetic testing but cleared for major aneuploidies (cases: n = 544, 57.7%) and control pregnancies (n = 399, 42.3%). Using genome-wide genotyping and RNA sequencing of first-trimester and term placental tissue, combined with medical information from registry data and maternal self-report data, we investigated potential negative medical outcomes and genetic susceptibility to disease and their correlates in placenta gene expression. Case mothers did not present with higher levels of depression, perceived stress, or anxiety during pregnancy. Case children were significantly diagnosed more often with congenital malformations of the circulatory system (4.12 (95% CI [1.22−13.93]) higher hazard) and presented with significantly more copy number duplications as compared to controls (burden analysis, based on all copy number variants (CNVs) with at most 10% frequency, 823 called duplications in 297 cases versus 626 called duplications in 277 controls, p = 0.01). Fifteen genes showed differential gene expression (FDR < 0.1) in association with congenital malformations in first-trimester but not term placenta. These were significantly enriched for genes associated with placental dysfunction. In spite of normal routine follow-up prenatal testing results in early pregnancy, case children presented with an increased likelihood of negative outcomes, which should prompt vigilance in follow-up during pregnancy and after birth.
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Affiliation(s)
- Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
| | - Cristiana Cruceanu
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Marius Lahti-Pulkkinen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Finnish Institute for Health and Welfare, 00271 Helsinki, Finland
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Linda Dieckmann
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
- International Max Planck Research School for Translational Psychiatry, 80804 Munich, Germany
| | - Maik Ködel
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
| | - Susann Sauer
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
| | - Monika Rex-Haffner
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
| | - Sara Sammallahti
- Department of Obstetrics and Gynaecology, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
| | - Eero Kajantie
- Finnish Institute for Health and Welfare, 00271 Helsinki, Finland
- Children’s Hospital, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
- Faculty of Medicine, PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, 90014 Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, 00014 Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
- Department of Obstetrics and Gynecology, Tampere University Hospital and Faculty of Medicine and Health Technology, Center for Child, Adolescent and Maternal Health Research, Tampere University, 33520 Tampere, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Elisabeth B. Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, Atlanta, GA 30322, USA
- Correspondence:
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Sufriyana H, Salim HM, Muhammad AR, Wu YW, Su ECY. Blood biomarkers representing maternal-fetal interface tissues used to predict early-and late-onset preeclampsia but not COVID-19 infection. Comput Struct Biotechnol J 2022; 20:4206-4224. [PMID: 35966044 PMCID: PMC9359600 DOI: 10.1016/j.csbj.2022.08.011] [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: 06/27/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 11/06/2022] Open
Abstract
Endothelial dysfunction misleads blood marker discovery by differential expression. Blood-derived surrogate transcriptome of target-tissue avoids the false discovery. ITGA5 implies polymicrobial infection of maternal-fetal interface in preeclampsia. ITGA5 and IRF6 implies viral co-infection in early-onset preeclampsia. ITGA5, IRF6, and P2RX7 differ imminent preeclampsia from COVID-19 infection.
Background A well-known blood biomarker (soluble fms-like tyrosinase-1 [sFLT-1]) for preeclampsia, i.e., a pregnancy disorder, was found to predict severe COVID-19, including in males. True biomarker may be masked by more-abrupt changes related to endothelial instead of placental dysfunction. This study aimed to identify blood biomarkers that represent maternal-fetal interface tissues for predicting preeclampsia but not COVID-19 infection. Methods The surrogate transcriptome of tissues was determined by that in maternal blood, utilizing four datasets (n = 1354) which were collected before the COVID-19 pandemic. Applying machine learning, a preeclampsia prediction model was chosen between those using blood transcriptome (differentially expressed genes [DEGs]) and the blood-derived surrogate for tissues. We selected the best predictive model by the area under the receiver operating characteristic (AUROC) using a dataset for developing the model, and well-replicated in datasets both with and without an intervention. To identify eligible blood biomarkers that predicted any-onset preeclampsia from the datasets but that were not positive in the COVID-19 dataset (n = 47), we compared several methods of predictor discovery: (1) the best prediction model; (2) gene sets of standard pipelines; and (3) a validated gene set for predicting any-onset preeclampsia during the pandemic (n = 404). We chose the most predictive biomarkers from the best method with the significantly largest number of discoveries by a permutation test. The biological relevance was justified by exploring and reanalyzing low- and high-level, multiomics information. Results A prediction model using the surrogates developed for predicting any-onset preeclampsia (AUROC of 0.85, 95 % confidence interval [CI] 0.77 to 0.93) was the only that was well-replicated in an independent dataset with no intervention. No model was well-replicated in datasets with a vitamin D intervention. None of the blood biomarkers with high weights in the best model overlapped with blood DEGs. Blood biomarkers were transcripts of integrin-α5 (ITGA5), interferon regulatory factor-6 (IRF6), and P2X purinoreceptor-7 (P2RX7) from the prediction model, which was the only method that significantly discovered eligible blood biomarkers (n = 3/100 combinations, 3.0 %; P =.036). Most of the predicted events (73.70 %) among any-onset preeclampsia were cluster A as defined by ITGA5 (Z-score ≥ 1.1), but were only a minority (6.34 %) among positives in the COVID-19 dataset. The remaining were predicted events (26.30 %) among any-onset preeclampsia or those among COVID-19 infection (93.66 %) if IRF6 Z-score was ≥-0.73 (clusters B and C), in which none was the predicted events among either late-onset preeclampsia (LOPE) or COVID-19 infection if P2RX7 Z-score was <0.13 (cluster C). Greater proportions of predicted events among LOPE were cluster A (82.85 % vs 70.53 %) compared to early-onset preeclampsia (EOPE). The biological relevance by multiomics information explained the biomarker mechanism, polymicrobial infection in any-onset preeclampsia by ITGA5, viral co-infection in EOPE by ITGA5-IRF6, a shared prediction with COVID-19 infection by ITGA5-IRF6-P2RX7, and non-replicability in datasets with a vitamin D intervention by ITGA5. Conclusions In a model that predicts preeclampsia but not COVID-19 infection, the important predictors were genes in maternal blood that were not extremely expressed, including the proposed blood biomarkers. The predictive performance and biological relevance should be validated in future experiments.
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Affiliation(s)
- Herdiantri Sufriyana
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Xing Street, Taipei 11031, Taiwan.,Department of Medical Physiology, Faculty of Medicine, Universitas Nahdlatul Ulama Surabaya, 57 Raya Jemursari Road, Surabaya 60237, Indonesia
| | - Hotimah Masdan Salim
- Department of Molecular Biology, Faculty of Medicine, Universitas Nahdlatul Ulama Surabaya, 57 Raya Jemursari Road, Surabaya 60237, Indonesia
| | - Akbar Reza Muhammad
- Faculty of Medicine, Universitas Nahdlatul Ulama Surabaya, 57 Raya Jemursari Road, Surabaya 60237, Indonesia
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Xing Street, Taipei 11031, Taiwan.,Clinical Big Data Research Center, Taipei Medical University Hospital, 250 Wu-Xing Street, Taipei 11031, Taiwan
| | - Emily Chia-Yu Su
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Xing Street, Taipei 11031, Taiwan.,Clinical Big Data Research Center, Taipei Medical University Hospital, 250 Wu-Xing Street, Taipei 11031, Taiwan.,Research Center for Artificial Intelligence in Medicine, Taipei Medical University, 250 Wu-Xing Street, Taipei 11031, Taiwan
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Liu Y, Lu X, Zhang Y, Liu M. Identification and Validation of a Five-Gene Diagnostic Signature for Preeclampsia. Front Genet 2022; 13:910556. [PMID: 35774506 PMCID: PMC9237423 DOI: 10.3389/fgene.2022.910556] [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: 04/01/2022] [Accepted: 05/27/2022] [Indexed: 11/29/2022] Open
Abstract
Preeclampsia is the leading cause of morbidity and mortality for mothers and newborns worldwide. Despite extensive efforts made to understand the underlying pathology of preeclampsia, there is still no clinically useful effective tool for the early diagnosis of preeclampsia. In this study, we conducted a retrospectively multicenter discover-validation study to develop and validate a novel biomarker for preeclampsia diagnosis. We identified 38 differentially expressed genes (DEGs) involved in preeclampsia in a case-control study by analyzing expression profiles in the discovery cohort. We developed a 5-mRNA signature (termed PE5-signature) to diagnose preeclampsia from 38 DEGs using recursive feature elimination with a random forest supervised classification algorithm, including ENG, KRT80, CEBPA, RDH13 and WASH9P. The PE5-signature showed high accuracy in discriminating preeclampsia from controls with a receiver operating characteristic area under the curve value (AUC) of 0.971, a sensitivity of 0.842 and a specificity of 0.950. The PE5-signature was then validated in an independent case-control study and achieved a reliable and robust predictive performance with an AUC of 0.929, a sensitivity of 0.696, and a specificity of 0.946. In summary, we have developed and validated a five-mRNA biomarker panel as a risk assessment tool to assist in the detection of preeclampsia. This gene panel has potential clinical value for early preeclampsia diagnosis and may help us better understand the precise mechanisms involved.
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Tamposis IA, Manios GA, Charitou T, Vennou KE, Kontou PI, Bagos PG. MAGE: An Open-Source Tool for Meta-Analysis of Gene Expression Studies. BIOLOGY 2022; 11:biology11060895. [PMID: 35741417 PMCID: PMC9220151 DOI: 10.3390/biology11060895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022]
Abstract
MAGE (Meta-Analysis of Gene Expression) is a Python open-source software package designed to perform meta-analysis and functional enrichment analysis of gene expression data. We incorporate standard methods for the meta-analysis of gene expression studies, bootstrap standard errors, corrections for multiple testing, and meta-analysis of multiple outcomes. Importantly, the MAGE toolkit includes additional features for the conversion of probes to gene identifiers, and for conducting functional enrichment analysis, with annotated results, of statistically significant enriched terms in several formats. Along with the tool itself, a web-based infrastructure was also developed to support the features of this package.
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Affiliation(s)
- Ioannis A. Tamposis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.A.T.); (G.A.M.); (T.C.); (K.E.V.)
| | - Georgios A. Manios
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.A.T.); (G.A.M.); (T.C.); (K.E.V.)
| | - Theodosia Charitou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.A.T.); (G.A.M.); (T.C.); (K.E.V.)
| | - Konstantina E. Vennou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.A.T.); (G.A.M.); (T.C.); (K.E.V.)
| | | | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.A.T.); (G.A.M.); (T.C.); (K.E.V.)
- Correspondence:
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Sobhani NC, Mernoff R, Abraha M, Okorie CN, Marquez-Magana L, Gaw SL, Robinson JF. Integrated analysis of transcriptomic datasets to identify placental biomarkers of spontaneous preterm birth. Placenta 2022; 122:66-73. [DOI: 10.1016/j.placenta.2022.03.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/06/2022] [Accepted: 03/22/2022] [Indexed: 11/28/2022]
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Celiksoy HY, Sozen H, Baktiroglu M, Topuz S, Salihoglu Y. The Etiology of Adnexal Masses in Women with a History of Non-Gynaecologic Malignancy: Recurrence, Second Primary or None? J Turk Ger Gynecol Assoc 2022; 23:8-13. [PMID: 35263833 PMCID: PMC8907436 DOI: 10.4274/jtgga.galenos.2021.2020-0224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Saei H, Govahi A, Abiri A, Eghbali M, Abiri M. Comprehensive transcriptome mining identified the gene expression signature and differentially regulated pathways of the late-onset preeclampsia. Pregnancy Hypertens 2021; 25:91-102. [PMID: 34098523 DOI: 10.1016/j.preghy.2021.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/11/2021] [Accepted: 05/08/2021] [Indexed: 01/18/2023]
Abstract
Preeclampsia (PE) is categorized as a pregnancy-related hypertensive disorder and is a serious concern in pregnancies. Several factors, including genetic factors (placenta gene expression, and imprinting), oxidative stress, the inaccurate immune response of the mother, and the environmental factors are responsible for PE development, but still, the exact mechanism of the pathogenesis has remained unknown. The main aim of the present study is to identify the gene expression signature in placenta tissue, to unveil disease etiology mechanisms. The GEO, PubMed, and ArrayExpress databases have selected to identify gene expression datasets on placenta samples of both preeclampsia and the normotensive controls. A comprehensive gene expression meta-analysis of fourteen publicly available microarray data of preeclampsia disease has performed to identify gene expression signature and responsible biological pathways and processes. Using two different meta-analysis pipeline (in-house and INMEX) we have identified a total of 1234 differentially expressed genes (DEGs) with in-house method, including 713 overexpressed and 356 under-expressed genes whereas 272 DEGs (131 over and 141 under-expressed) have identified with INMEX, across PEs and healthy controls. Comprehensive functional enrichment and pathway analysis was performed by EnrichR library, whic revealed "Asparagine N-linked glycosylation Homo sapiens", "Nef and signal transduction", "Hemostasis", and "immune system" among the most enriched terms. The present study sets out to explain a novel database of candidate genetic markers and biological pathways that play a critical role in PE development, which might aid in the identification of diagnostic, prognostic, and therapeutic informative molecules.
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Affiliation(s)
- Hassan Saei
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Govahi
- Department of Medical Immunology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ameneh Abiri
- Perinatology Department, Arash Women's Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Eghbali
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Abiri
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran; Shahid Akbarabadi Clinical Research Development Unit (ShACRDU), Iran University of Medical Sciences, Tehran, Iran.
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