1
|
Zhang R, Du J, Xiao Z, Jiang Y, Jin L, Weng Q. Association between the peripartum maternal and fetal telomere lengths and mitochondrial DNA copy numbers and preeclampsia: a prospective case-control study. BMC Pregnancy Childbirth 2022; 22:483. [PMID: 35698093 PMCID: PMC9195426 DOI: 10.1186/s12884-022-04801-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose To explore changes in telomere length (TL) and mitochondrial copy number (mtDNA-CN) in preeclampsia (PE) and to evaluate the combined effect of maternal TL and mtDNA-CN on PE risk. Methods A case–control study of 471 subjects (130 PE cases and 341 age frequency matched controls with gestational age rank from 24 to 42 weeks) was conducted in Nanjing Drum Tower Hospital, Jiangsu Province of China. Relative telomere length (RTL) and mtDNA-CN were measured using quantitative polymerase chain reaction (qPCR), and PE risk was compared between groups by logistic regression analyses. Results PE patients displayed longer RTL (0.48 versus 0.30) and higher mtDNA-CN (3.02 versus 2.00) in maternal blood as well as longer RTL (0.61 versus 0.35) but lower mtDNA-CN (1.69 versus 5.49) in cord blood (all p < 0.001). Exercise during pregnancy exerted an obvious effect of maternal telomere length prolongation. Multiparous women with folic acid intake during early pregnancy and those who delivered vaginally showed longer telomere length, while those factors imposed no or opposite effect on RTL in PE cases. Furthermore, RTL and mtDNA-CN were positively correlated in controls (in maternal blood r = 0.18, p < 0.01; in cord blood r = 0.19, p < 0.001), but this correlation was disrupted in PE patients in both maternal blood and cord blood. Longer maternal RTL and higher mtDNA-CN were associated with a higher risk of PE, and the ROC curve of RTL and mtDNA-CN for predicting PE risk presented an AUC of 0.755 (95% CI: 0.698–0.812). Conclusions The interaction of TL and mtDNA-CN may play an important role in the pathogenesis of PE and could be a potential biomarker of PE risk. Supplementary information The online version contains supplementary material available at 10.1186/s12884-022-04801-0.
Collapse
Affiliation(s)
- Ruyi Zhang
- Department of Obstetrics & Gynecology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Department of Obstetrics & Gynecology, Drum Tower Clinical Medical College, Nanjing Medical University, Nanjing, 210008, China.,Department of Obstetrics & Gynecology, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210008, China.,Department of Obstetrics & Gynecology, Nanjing Drum Tower Hospital Clinical College of Xuzhou Medical University, Nanjing, 210008, China
| | - Jiangbo Du
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,StateKey Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zhendong Xiao
- Department of Obstetrics & Gynecology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Yuan Jiang
- Department of Obstetrics & Gynecology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Liang Jin
- Department of Obstetrics & Gynecology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Qiao Weng
- Department of Obstetrics & Gynecology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China. .,Department of Obstetrics & Gynecology, Drum Tower Clinical Medical College, Nanjing Medical University, Nanjing, 210008, China. .,Department of Obstetrics & Gynecology, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210008, China. .,Department of Obstetrics & Gynecology, Nanjing Drum Tower Hospital Clinical College of Xuzhou Medical University, Nanjing, 210008, China.
| |
Collapse
|
2
|
Liu Y. scDeconv: an R package to deconvolve bulk DNA methylation data with scRNA-seq data and paired bulk RNA-DNA methylation data. Brief Bioinform 2022; 23:6572659. [PMID: 35453146 PMCID: PMC9271220 DOI: 10.1093/bib/bbac150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/26/2022] [Accepted: 04/04/2022] [Indexed: 11/14/2022] Open
Abstract
Many DNA methylation (DNAm) data are from tissues composed of various cell types, and hence cell deconvolution methods are needed to infer their cell compositions accurately. However, a bottleneck for DNAm data is the lack of cell-type-specific DNAm references. On the other hand, scRNA-seq data are being accumulated rapidly with various cell-type transcriptomic signatures characterized, and also, many paired bulk RNA-DNAm data are publicly available currently. Hence, we developed the R package scDeconv to use these resources to solve the reference deficiency problem of DNAm data and deconvolve them from scRNA-seq data in a trans-omics manner. It assumes that paired samples have similar cell compositions. So the cell content information deconvolved from the scRNA-seq and paired RNA data can be transferred to the paired DNAm samples. Then an ensemble model is trained to fit these cell contents with DNAm features and adjust the paired RNA deconvolution in a co-training manner. Finally, the model can be used on other bulk DNAm data to predict their relative cell-type abundances. The effectiveness of this method is proved by its accurate deconvolution on the three testing datasets here, and if given an appropriate paired dataset, scDeconv can also deconvolve other omics, such as ATAC-seq data. Furthermore, the package also contains other functions, such as identifying cell-type-specific inter-group differential features from bulk DNAm data. scDeconv is available at: https://github.com/yuabrahamliu/scDeconv.
Collapse
Affiliation(s)
- Yu Liu
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| |
Collapse
|
3
|
Farrukh S, Baig S, Hussain R, Shahid A, Khan ST. Telomere reprogramming during fetal life in low socioeconomic mothers. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2019. [DOI: 10.1186/s43042-019-0007-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
4
|
Fitzgerald W, Gomez-Lopez N, Erez O, Romero R, Margolis L. Extracellular vesicles generated by placental tissues ex vivo: A transport system for immune mediators and growth factors. Am J Reprod Immunol 2018; 80:e12860. [PMID: 29726582 PMCID: PMC6021205 DOI: 10.1111/aji.12860] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/12/2022] Open
Abstract
PROBLEM To study the mechanisms of placenta function and the role of extracellular vesicles (EVs) in pregnancy, it is necessary to develop an ex vivo system that retains placental cytoarchitecture and the primary metabolic aspects, in particular the release of EVs and soluble factors. Here, we developed such a system and investigated the pattern of secretion of cytokines, growth factors, and extracellular vesicles by placental villous and amnion tissues ex vivo. METHODS OF STUDY Placental villous and amnion explants were cultured for 2 weeks at the air/liquid interface and their morphology and the released cytokines and EVs were analyzed. Cytokines were analyzed with multiplexed bead assays, and individual EVs were analyzed with recently developed techniques that involved EV capture with magnetic nanoparticles coupled to anti-EV antibodies and flow cytometry. RESULTS Ex vivo tissues (i) remained viable and preserved their cytoarchitecture; (ii) maintained secretion of cytokines and growth factors; (iii) released EVs of syncytiotrophoblast and amnion epithelial cell origins that contain cytokines and growth factors. CONCLUSION A system of ex vivo placental villous and amnion tissues can be used as an adequate model to study placenta metabolic activity in normal and complicated pregnancies, in particular to characterize EVs by their surface markers and by encapsulated proteins. Establishment and benchmarking the placenta ex vivo system may provide new insight in the functional status of this organ in various placental disorders, particularly regarding the release of EVs and cytokines. Such EVs may have a prognostic value for pregnancy complications.
Collapse
Affiliation(s)
- Wendy Fitzgerald
- Section of Intercellular Interactions, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI
| | - 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, Bethesda, MD, and Detroit, MI
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Immunology, Microbiology and Biochemistry, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - 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, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI
- 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
| | - Leonid Margolis
- Section of Intercellular Interactions, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI
| |
Collapse
|
5
|
Entringer S, de Punder K, Buss C, Wadhwa PD. The fetal programming of telomere biology hypothesis: an update. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170151. [PMID: 29335381 PMCID: PMC5784074 DOI: 10.1098/rstb.2017.0151] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2017] [Indexed: 12/17/2022] Open
Abstract
Research on mechanisms underlying fetal programming of health and disease risk has focused primarily on processes that are specific to cell types, organs or phenotypes of interest. However, the observation that developmental conditions concomitantly influence a diverse set of phenotypes, the majority of which are implicated in age-related disorders, raises the possibility that such developmental conditions may additionally exert effects via a common underlying mechanism that involves cellular/molecular ageing-related processes. In this context, we submit that telomere biology represents a process of particular interest in humans because, firstly, this system represents among the most salient antecedent cellular phenotypes for common age-related disorders; secondly, its initial (newborn) setting appears to be particularly important for its long-term effects; and thirdly, its initial setting appears to be plastic and under developmental regulation. We propose that the effects of suboptimal intrauterine conditions on the initial setting of telomere length and telomerase expression/activity capacity may be mediated by the programming actions of stress-related maternal-placental-fetal oxidative, immune, endocrine and metabolic pathways in a manner that may ultimately accelerate cellular dysfunction, ageing and disease susceptibility over the lifespan. This perspectives paper provides an overview of each of the elements underlying this hypothesis, with an emphasis on recent developments, findings and future directions.This article is part of the theme issue 'Understanding diversity in telomere dynamics'.
Collapse
Affiliation(s)
- Sonja Entringer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Medical Psychology, Berlin, Germany
- Department of Pediatrics, University of California, School of Medicine, Irvine, CA, USA
- Development, Health and Disease Research Program, University of California, School of Medicine, Irvine, CA, USA
| | - Karin de Punder
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Medical Psychology, Berlin, Germany
| | - Claudia Buss
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Medical Psychology, Berlin, Germany
- Department of Pediatrics, University of California, School of Medicine, Irvine, CA, USA
- Development, Health and Disease Research Program, University of California, School of Medicine, Irvine, CA, USA
| | - Pathik D Wadhwa
- Department of Psychiatry and Human Behavior, University of California, School of Medicine, Irvine, CA, USA
- Department of Obstetrics and Gynecology, University of California, School of Medicine, Irvine, CA, USA
- Department of Pediatrics, University of California, School of Medicine, Irvine, CA, USA
- Department of Epidemiology, University of California, School of Medicine, Irvine, CA, USA
- Development, Health and Disease Research Program, University of California, School of Medicine, Irvine, CA, USA
| |
Collapse
|
6
|
Rahat B, Hamid A, Ahmad Najar R, Bagga R, Kaur J. Epigenetic mechanisms regulate placental c-myc and hTERT in normal and pathological pregnancies; c-myc as a novel fetal DNA epigenetic marker for pre-eclampsia. Mol Hum Reprod 2014; 20:1026-1040. [PMID: 25024139 DOI: 10.1093/molehr/gau053] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024] Open
Abstract
Placental development is known for its resemblance with tumor development, such as in the expression of oncogenes (c-myc) and telomerase (hTERT). The expression of c-myc and hTERT is up-regulated during early pregnancy and gestational trophoblastic diseases (GTDs). To determine the role of DNA methylation [via methylation-sensitive high resolution melting (MS-HRM)] and histone modifications [via chromatin immunoprecipitation (ChIP assay)] in regulating the differential expression of c-myc and hTERT during normal gestation and their dysregulation during placental disorders, we obtained placental samples from 135 pregnant women, in five groups: normal first, second and third trimester (n = 30 each), pre-eclamptic pregnancy (n = 30) and molar pregnancy (n = 15). Two placental cell lines (JEG-3 and HTR-8/SVneo) and isolated first-trimester cytotrophoblasts were also studied. Quantitative RT-PCR revealed decreased mRNA expression levels of c-myc and hTERT, which were associated with a higher level of H3K9me3 (1.5-fold, P < 0.05) and H3K27me3 (1.9-fold, P < 0.05), respectively, in third-trimester placental villi versus first-trimester villi. A significantly lower level of H3K27me3 in molar placenta was associated with a higher mRNA expression of c-myc and hTERT. The development of pre-eclampsia (PE) was associated with increased methylation (P < 0.001) and H3K27me3 (P < 0.01) at the c-myc promoter and reduced H3K9me3 (P < 0.01) and H3K27me3 (P < 0.05) at the hTERT promoter. Further, mRNA expression of c-myc and hTERT was strongly correlated in molar villi (r = 0.88, P < 0.01) and JEG-3 cells (r = 0.99, P < 0.02). Moreover, on the basis of methylation data, we demonstrate the potential of c-myc as a fetal DNA epigenetic marker for pre-eclamptic pregnancies. Thus we suggest a role for epigenetic mechanisms in regulating differential expression of c-myc and hTERT during placental development and use of the c-myc promoter region as a potential fetal DNA marker in the case of PE.
Collapse
Affiliation(s)
- Beenish Rahat
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Abid Hamid
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Rauf Ahmad Najar
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Rashmi Bagga
- Department of Obstetrics and Gynaecology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Jyotdeep Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| |
Collapse
|