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Coppedè F, Bhaduri U, Stoccoro A, Nicolì V, Di Venere E, Merla G. DNA Methylation in the Fields of Prenatal Diagnosis and Early Detection of Cancers. Int J Mol Sci 2023; 24:11715. [PMID: 37511475 PMCID: PMC10380460 DOI: 10.3390/ijms241411715] [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: 05/31/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The central objective of the metamorphosis of discovery science into biomedical applications is to serve the purpose of patients and curtail the global disease burden. The journey from the discovery of DNA methylation (DNAm) as a biological process to its emergence as a diagnostic tool is one of the finest examples of such metamorphosis and has taken nearly a century. Particularly in the last decade, the application of DNA methylation studies in the clinic has been standardized more than ever before, with great potential to diagnose a multitude of diseases that are associated with a burgeoning number of genes with this epigenetic alteration. Fetal DNAm detection is becoming useful for noninvasive prenatal testing, whereas, in very preterm infants, DNAm is also shown to be a potential biological indicator of prenatal risk factors. In the context of cancer, liquid biopsy-based DNA-methylation profiling is offering valuable epigenetic biomarkers for noninvasive early-stage diagnosis. In this review, we focus on the applications of DNA methylation in prenatal diagnosis for delivering timely therapy before or after birth and in detecting early-stage cancers for better clinical outcomes. Furthermore, we also provide an up-to-date commercial landscape of DNAm biomarkers for cancer detection and screening of cancers of unknown origin.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
- Interdepartmental Research Center of Biology and Pathology of Aging, University of Pisa, 56126 Pisa, Italy
| | - Utsa Bhaduri
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Vanessa Nicolì
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Eleonora Di Venere
- Department of Molecular Medicine & Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
- Department of Molecular Medicine & Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
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Korostin DO, Plakhina DA, Belova VA. Noninvasive prenatal testing: the aspects of its introduction into clinical practice. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The last couple of years have witnessed the rapid development of prenatal molecular-based screening for fetal aneuploidies that utilizes the analysis of cell-free DNA circulating in the bloodstream of a pregnant woman. The present review looks at the potential and limitations of such testing and the possible causes of false-positive and false-negative results. The review also describes the underlying principles of data acquisition and analysis the testing involves. In addition, we talk about the opinions held by the expert community and some aspects of legislation on the use of noninvasive prenatal testing (NIPT) in clinical practice in the countries where NIPT is much more widespread than in Russia.
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Affiliation(s)
- D. O. Korostin
- Pirogov Russian National Research Medical University, Moscow, Russia; Genotek Ltd., Moscow, Russia
| | | | - V. A. Belova
- Pirogov Russian National Research Medical University, Moscow, Russia; Genotek Ltd., Moscow, Russia
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Kazemi M, Salehi M, Kheirollahi M. MeDIP Real-Time qPCR has the Potential for Noninvasive Prenatal Screening of Fetal Trisomy 21. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2017; 6:13-21. [PMID: 28868265 PMCID: PMC5568188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/01/2017] [Indexed: 11/25/2022]
Abstract
This study aimed to verify the reliability of the 7 tissue differentially methylated regions used in the methylated DNA immunoprecipitation (MeDIP) real- time quantitative polymerase chain reaction (real-time qPCR) based approach of fetal DNA in maternal blood to diagnosis of fetal trisomy 21. Forty pregnant women with high risk pregnancy who were referred after first or second trimester screening tests, were selected randomly. For each sample whole DNA extraction (mother and fetus), fragmentation of DNA, immunoprecipitation of methylated DNA and real- time qPCR using 7 primer pairs was performed. D-value for each sample was calculated using the following formula D = -4.908+ 0.254 XEP1+ 0.409 XEP4+ 0.793 XEP5+ 0.324 XEP6+ 0.505 XEP7+ 0.508 XEP9+ 0.691 XEP12. In all normal cases, D value was negative, while it was positive in all trisomy cases. Therefore, all normal and trisomy 21 cases were classified correctly which correspond to 100% specificity and 100% sensitivity for this method. The MeDIP real-time qPCR method has provided the opportunity for noninvasive prenatal diagnosis of fetal trisomy 21 to be potentially employed into the routine practice of diagnostic laboratories.
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Affiliation(s)
- Mohammad Kazemi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Medical Genetic Center of Genome, Isfahan, Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommuni-cable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Mansoor Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Medical Genetic Center of Genome, Isfahan, Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommuni-cable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.,Corresponding author: Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran. E. mail: .
| | - Majid Kheirollahi
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommuni-cable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.
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Affiliation(s)
- Felix C.K. Wong
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, and
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; ,
| | - Y.M. Dennis Lo
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, and
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; ,
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Christopoulou G, Papageorgiou EA, Patsalis PC, Velissariou V. Comparison of next generation sequencing-based and methylated DNA immunoprecipitation-based approaches for fetal aneuploidy non-invasive prenatal testing. World J Med Genet 2015; 5:23-27. [DOI: 10.5496/wjmg.v5.i2.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 04/07/2015] [Accepted: 04/20/2015] [Indexed: 02/06/2023] Open
Abstract
Over the past few years, many researchers have attempted to develop non-invasive prenatal testing methods in order to investigate the genetic status of the fetus. The aim is to avoid invasive procedures such as chorionic villus and amniotic fluid sampling, which result in a significant risk for pregnancy loss. The discovery of cell free fetal DNA circulating in the maternal blood has great potential for the development of non-invasive prenatal testing (NIPT) methodologies. Such strategies have been successfully applied for the determination of the fetal rhesus status and inherited monogenic disease but the field of fetal aneuploidy investigation seems to be more challenging. The main reason for this is that the maternal cell free DNA in the mother’s plasma is far more abundant, and because it is identical to half of the corresponding fetal DNA. Approaches developed are mainly based on next generation sequencing (NGS) technologies and epigenetic genetic modifications, such as fetal-maternal DNA differential methylation. At present, genetic services for non-invasive fetal aneuploidy detection are offered using NGS-based approaches but, for reasons that are presented herein, they still serve as screening tests which are not readily accessed by the majority of couples. Here we discuss the limitations of both strategies for NIPT and the future potential of the methods developed.
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Bioinformatics analysis of circulating cell-free DNA sequencing data. Clin Biochem 2015; 48:962-75. [PMID: 25966961 DOI: 10.1016/j.clinbiochem.2015.04.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/30/2015] [Accepted: 04/29/2015] [Indexed: 12/18/2022]
Abstract
The discovery of cell-free DNA molecules in plasma has opened up numerous opportunities in noninvasive diagnosis. Cell-free DNA molecules have become increasingly recognized as promising biomarkers for detection and management of many diseases. The advent of next generation sequencing has provided unprecedented opportunities to scrutinize the characteristics of cell-free DNA molecules in plasma in a genome-wide fashion and at single-base resolution. Consequently, clinical applications of circulating cell-free DNA analysis have not only revolutionized noninvasive prenatal diagnosis but also facilitated cancer detection and monitoring toward an era of blood-based personalized medicine. With the remarkably increasing throughput and lowering cost of next generation sequencing, bioinformatics analysis becomes increasingly demanding to understand the large amount of data generated by these sequencing platforms. In this Review, we highlight the major bioinformatics algorithms involved in the analysis of cell-free DNA sequencing data. Firstly, we briefly describe the biological properties of these molecules and provide an overview of the general bioinformatics approach for the analysis of cell-free DNA. Then, we discuss the specific upstream bioinformatics considerations concerning the analysis of sequencing data of circulating cell-free DNA, followed by further detailed elaboration on each key clinical situation in noninvasive prenatal diagnosis and cancer management where downstream bioinformatics analysis is heavily involved. We also discuss bioinformatics analysis as well as clinical applications of the newly developed massively parallel bisulfite sequencing of cell-free DNA. Finally, we offer our perspectives on the future development of bioinformatics in noninvasive diagnosis.
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Ou X, Wang H, Qu D, Chen Y, Gao J, Sun H. Epigenome-wide DNA methylation assay reveals placental epigenetic markers for noninvasive fetal single-nucleotide polymorphism genotyping in maternal plasma. Transfusion 2014; 54:2523-33. [PMID: 24749853 DOI: 10.1111/trf.12659] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/14/2014] [Accepted: 02/19/2014] [Indexed: 01/03/2023]
Abstract
BACKGROUND The use of DNA methylation difference between maternal blood cell and fetal (placental) DNA is one of the main areas of interest for the development of fetal epigenetics markers in maternal plasma. STUDY DESIGN AND METHODS We employed a methylation array (HumanMethylation450 array, Illumina, Inc.) to identify novel biomarkers that are specially hypermethylated in placental DNA versus maternal blood cells in a genome-wide basis. Validation by bisulfite genomic sequencing was performed and the priority was given to potential targets that harbor differential methylated CpG sites overlapped with at least two methylation-sensitive restriction enzyme (MSRE) recognizing sites, as well as one polymorphic single-nucleotide polymorphism (SNP), within a short DNA stretch. Three candidate regions of PSMB8, SKI, and CHST11 gene were selected for developing a preliminary polymerase chain reaction assay with MSRE digestion of maternal plasma DNA. SNP genotypes were confirmed by direct sequencing. RESULTS We identified 2944 and 5218 fetal-specific hypermethylated CpG sites in the first- and third-trimester placenta, respectively, of which 2613 were overlapped, suggesting a consistency of differential methylation during the whole pregnancy. The array results were confirmed by bisulfite genomic sequencing. The preliminary tests in maternal plasma showed that postdigestion hypermathylated versions of these candidate molecules were detectable only in pregnant women. We further revealed that methylated targets in maternal plasma possessed the fetal SNP genotypes. CONCLUSION The present studies systematically identified hypermethylated sites in fetal tissues and preliminarily demonstrated that some of the fetal epigenetic markers that contain informative SNPs have great potential for noninvasive fetal genetic diagnosis.
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Affiliation(s)
- Xueling Ou
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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Papageorgiou EA, Koumbaris G, Kypri E, Hadjidaniel M, Patsalis PC. The Epigenome View: An Effort towards Non-Invasive Prenatal Diagnosis. Genes (Basel) 2014; 5:310-29. [PMID: 24722507 PMCID: PMC4094935 DOI: 10.3390/genes5020310] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/05/2014] [Accepted: 03/27/2014] [Indexed: 02/06/2023] Open
Abstract
Epigenetic modifications have proven to play a significant role in cancer development, as well as fetal development. Taking advantage of the knowledge acquired during the last decade, great interest has been shown worldwide in deciphering the fetal epigenome towards the development of methylation-based non-invasive prenatal tests (NIPT). In this review, we highlight the different approaches implemented, such as sodium bisulfite conversion, restriction enzyme digestion and methylated DNA immunoprecipitation, for the identification of differentially methylated regions (DMRs) between free fetal DNA found in maternal blood and DNA from maternal blood cells. Furthermore, we evaluate the use of selected DMRs identified towards the development of NIPT for fetal chromosomal aneuploidies. In addition, we perform a comparison analysis, evaluate the performance of each assay and provide a comprehensive discussion on the potential use of different methylation-based technologies in retrieving the fetal methylome, with the aim of further expanding the development of NIPT assays.
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Affiliation(s)
| | - George Koumbaris
- NIPD Genetics Ltd., Neas Engomis 31, Engomi, Nicosia 2409, Cyprus.
| | - Elena Kypri
- NIPD Genetics Ltd., Neas Engomis 31, Engomi, Nicosia 2409, Cyprus.
| | - Michael Hadjidaniel
- The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, Ayios Dometios, Nicosia 2370, Cyprus.
| | - Philippos C Patsalis
- The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, Ayios Dometios, Nicosia 2370, Cyprus.
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Provençal N, Suderman MJ, Guillemin C, Vitaro F, Côté SM, Hallett M, Tremblay RE, Szyf M. Association of childhood chronic physical aggression with a DNA methylation signature in adult human T cells. PLoS One 2014; 9:e89839. [PMID: 24691403 PMCID: PMC3972178 DOI: 10.1371/journal.pone.0089839] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 01/27/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Chronic physical aggression (CPA) is characterized by frequent use of physical aggression from early childhood to adolescence. Observed in approximately 5% of males, CPA is associated with early childhood adverse environments and long-term negative consequences. Alterations in DNA methylation, a covalent modification of DNA that regulates genome function, have been associated with early childhood adversity. AIMS To test the hypothesis that a trajectory of chronic physical aggression during childhood is associated with a distinct DNA methylation profile during adulthood. METHODS We analyzed genome-wide promoter DNA methylation profiles of T cells from two groups of adult males assessed annually for frequency of physical aggression between 6 and 15 years of age: a group with CPA and a control group. Methylation profiles covering the promoter regions of 20 000 genes and 400 microRNAs were generated using MeDIP followed by hybridization to microarrays. RESULTS In total, 448 distinct gene promoters were differentially methylated in CPA. Functionally, many of these genes have previously been shown to play a role in aggression and were enriched in biological pathways affected by behavior. Their locations in the genome tended to form clusters spanning millions of bases in the genome. CONCLUSIONS This study provides evidence of clustered and genome-wide variation in promoter DNA methylation in young adults that associates with a history of chronic physical aggression from 6 to 15 years of age. However, longitudinal studies of methylation during early childhood will be necessary to determine if and how this methylation variation in T cells DNA plays a role in early development of chronic physical aggression.
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Affiliation(s)
- Nadine Provençal
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Research Unit on Children's Psycho-Social Maladjustment and Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Canada
- Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec, Canada
| | - Matthew J. Suderman
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec, Canada
- McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
| | - Claire Guillemin
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Research Unit on Children's Psycho-Social Maladjustment and Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Canada
- Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec, Canada
| | - Frank Vitaro
- Research Unit on Children's Psycho-Social Maladjustment and Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Canada
- School of Psycho-Education, University of Montreal, Montréal, Quebec, Canada
| | - Sylvana M. Côté
- Research Unit on Children's Psycho-Social Maladjustment and Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Canada
- School of Social and Preventive Medicine, University of Montreal, Montréal, Quebec, Canada
| | - Michael Hallett
- McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
| | - Richard E. Tremblay
- Research Unit on Children's Psycho-Social Maladjustment and Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Canada
- Department of Psychology and Pediatrics, University of Montreal, Montreal, Quebec, Canada
- School of Public Health, Physiotherapy and Population Sciences, University College Dublin, Dublin, Ireland
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec, Canada
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Yin YZ, She Q, Zhang J, Zhang PZ, Zhang Y, Lin JW, Ye YC. Placental methylation markers in normal and trisomy 21 tissues. Prenat Diagn 2013; 34:63-70. [PMID: 24166080 DOI: 10.1002/pd.4256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 09/08/2013] [Accepted: 10/09/2013] [Indexed: 11/06/2022]
Abstract
OBJECTIVE The objective of this study is to combine multiplex ligation-dependent probe amplification (MLPA) and bisulfite sequencing to determine DNA methylation markers for noninvasive prenatal diagnosis of Down syndrome. METHODS DNA methylation ratios (MR) of four fragments (CGI149, CGI045, HLCS-1, and HLCS-2) on chromosome 21 were evaluated in blood cells from 13 nonpregnant women, 15 euploidies, and 11 Down Syndrome (DS) placentae. Ratios were measured by bisulfite sequencing and methylation-specific (MS)-MLPA. RESULTS The MS-MLPA and bisulfite sequencing results were concordant. CGI149, CGI045, and HLCS-2 were unmethylated in all nonpregnant blood cells. CGI149, CGI045, HLCS-1, and HLCS-2 were methylated in most of the euploid (13, 11, 15, and 15, respectively) and DS placentae (10, 11, 11, and 11, respectively). The median placental DNA MR in CGI149 was 0.4578 (interquartile range, 0.3568-0.5169) and 0.5918 (interquartile range, 0.5618-0.6659) in euploid and DS placentae, respectively (p = 0.001). Using placental MR at 0.5390 as a threshold, we detected DS at 90.9% sensitivity and 93.3% specificity. CONCLUSION The MS-MLPA is an effective alternative to bisulfite sequencing in assessing placental MR. CGI149 is a potential marker for the noninvasive diagnosis of Down syndrome.
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Affiliation(s)
- Yu-Zhu Yin
- Department of Obstetrics and Gynecology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Sandoval J, Peiró-Chova L, Pallardó FV, García-Giménez JL. Epigenetic biomarkers in laboratory diagnostics: emerging approaches and opportunities. Expert Rev Mol Diagn 2013; 13:457-71. [PMID: 23782253 DOI: 10.1586/erm.13.37] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetics has emerged as a new and promising field in recent years. Lifestyle, stress, drugs, physiopathological situations and pharmacological interventions have a great impact on the epigenetic code of the cells by altering the methylome, miRNA expression and the covalent histone modifications. Since there exists a need to find new biomarkers and improve diagnosis for several diseases, the research on epigenetic biomarkers for molecular diagnostics encourages the translation of this field from the bench to clinical practice. In this context, deciphering intricate epigenetic modifications involved in several molecular processes is a challenge that will be solved in the near future. In this review, the authors present an overview of the high-throughput technologies and laboratory techniques available for epigenetic studies, and also discuss which of them are more reliable to be used in a clinical diagnostic laboratory. In addition, the authors describe the most promising epigenetic biomarkers in lung, colorectal and prostate cancer, in which most advances have been achieved. Finally, the authors describe epigenetic biomarkers in some rare diseases; these rare syndromes are paradigms for a specific impaired molecular pathway, thus providing valuable information on the discovery of new epigenetic biomarkers.
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Affiliation(s)
- Juan Sandoval
- Epigenetics and Cancer Biology, Institut d'Investigació Biomèdica de Bellvitge IDIBELL, Barcelona, Spain
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Lee DE, Kim SY, Lim JH, Park SY, Ryu HM. Non-invasive prenatal testing of trisomy 18 by an epigenetic marker in first trimester maternal plasma. PLoS One 2013; 8:e78136. [PMID: 24223769 PMCID: PMC3815335 DOI: 10.1371/journal.pone.0078136] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/09/2013] [Indexed: 12/14/2022] Open
Abstract
Background Quantification of cell-free fetal DNA by methylation-based DNA discrimination has been used in non-invasive prenatal testing of fetal chromosomal aneuploidy. The maspin (Serpin peptidase inhibitor, clade B (ovalbumin), member 5; SERPINB5) gene, located on chromosome 18q21.33, is hypomethylated in the placenta and completely methylated in maternal blood cells. The objective of this study was to evaluate the accuracy of non-invasive detection of fetal trisomy 18 using the unmethylated-maspin (U-maspin) gene as a cell-free fetal DNA marker and the methylated-maspin (M-maspin) gene as a cell-free total DNA marker in the first trimester of pregnancy. Methodology/Principal Findings A nested case-control study was conducted using maternal plasma collected from 66 pregnant women, 11 carrying fetuses with trisomy 18 and 55 carrying normal fetuses. Median U-maspin concentrations were significantly elevated in women with trisomy 18 fetuses compared with controls (27.2 vs. 6.7 copies/mL; P<0.001). Median M-maspin concentrations were also significantly higher in women with trisomy 18 fetuses than in controls (96.9 vs. 19.5 copies/mL, P<0.001). The specificities of U-maspin and M-maspin concentrations for non-invasive fetal trisomy 18 detection were 96.4% and 74.5%, respectively, with a sensitivity of 90.9%. Conclusions Our results suggest that U-maspin and M-maspin concentrations may be useful as potential biomarkers for non-invasive detection of fetal trisomy 18 in the first trimester of pregnancy, irrespective of the sex and genetic variations of the fetus.
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Affiliation(s)
- Da Eun Lee
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women’s Healthcare Center, Seoul, Korea
| | - Shin Young Kim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women’s Healthcare Center, Seoul, Korea
| | - Ji Hyae Lim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women’s Healthcare Center, Seoul, Korea
| | - So Yeon Park
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women’s Healthcare Center, Seoul, Korea
| | - Hyun Mee Ryu
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women’s Healthcare Center, Seoul, Korea
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women’s Healthcare Center, Kwandong University College of Medicine, Seoul, Korea
- * E-mail:
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Non invasive prenatal diagnosis of aneuploidy: next generation sequencing or fetal DNA enrichment? Balkan J Med Genet 2013; 15:17-26. [PMID: 24052738 PMCID: PMC3776677 DOI: 10.2478/v10034-012-0013-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Current invasive procedures [amniocentesis and chorionic villus sampling (CVS)] pose a risk to mother and fetus and such diagnostic procedures are available only to high risk pregnancies limiting aneuploidy detection rate. This review seeks to highlight the necessity of investing in non invasive prenatal diagnosis (NIPD) and how NIPD would improve patient safety and detection rate as well as allowing detection earlier in pregnancy. Non invasive prenatal diagnosis can take either a proteomics approach or nucleic acid-based approach; this review focuses on the latter. Since the discovery of cell free fetal DNA (cffDNA) and fetal RNA in maternal plasma, procedures have been developed for detection for monogenic traits and for some have become well established (e.g., RHD blood group status). However, NIPD of aneuploidies remains technically challenging. This review examines currently published literature evaluating techniques and approaches that have been suggested and developed for aneuploidy detection, highlighting their advantages and limitations and areas for further research.
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Ou X, Gao J, Chen Y, Gao Y, Qu D, Sun H. Detecting hypermethylated fetalRASSF1Asequences in maternal plasma: implications for noninvasive paternity testing in pregnancy. Transfusion 2013; 53:1856-8. [DOI: 10.1111/trf.12246] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xueling Ou
- Department of Forensic Medicine; Zhongshan School of Medicine; Sun Yat-sen University
| | - Jun Gao
- Reproductive Medicine Center; First Affiliated Hospital of Sun Yat-sen University
| | - Yongzhen Chen
- Fetal Medicine Center; Department of Obstetrics and Gynecology; First Affiliated Hospital of Sun Yat-sen University
| | - Yu Gao
- Fetal Medicine Center; Department of Obstetrics and Gynecology; First Affiliated Hospital of Sun Yat-sen University
| | - Dongyang Qu
- Department of Forensic Medicine; Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou; China
| | - Hongyu Sun
- Department of Forensic Medicine; Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou; China
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The signature of maternal rearing in the methylome in rhesus macaque prefrontal cortex and T cells. J Neurosci 2013; 32:15626-42. [PMID: 23115197 DOI: 10.1523/jneurosci.1470-12.2012] [Citation(s) in RCA: 262] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Early-life adversity is associated with a broad scope of life-long health and behavioral disorders. Particularly critical is the role of the mother. A possible mechanism is that these effects are mediated by "epigenetic" mechanisms. Studies in rodents suggest a causal relationship between early-life adversity and changes in DNA methylation in several "candidate genes" in the brain. This study examines whether randomized differential rearing (maternal vs surrogate-peer rearing) of rhesus macaques is associated with differential methylation in early adulthood. The data presented here show that differential rearing leads to differential DNA methylation in both prefrontal cortex and T cells. These differentially methylated promoters tend to cluster by both chromosomal region and gene function. The broad impact of maternal rearing on DNA methylation in both the brain and T cells supports the hypothesis that the response to early-life adversity is system-wide and genome-wide and persists to adulthood. Our data also point to the feasibility of studying the impact of the social environment in peripheral T-cell DNA methylation.
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Novakovic B, Saffery R. The ever growing complexity of placental epigenetics – Role in adverse pregnancy outcomes and fetal programming. Placenta 2012; 33:959-70. [DOI: 10.1016/j.placenta.2012.10.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/02/2012] [Accepted: 10/06/2012] [Indexed: 02/01/2023]
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Eckmann-Scholz C, Bens S, Kolarova J, Schneppenheim S, Caliebe A, Heidemann S, von Kaisenberg C, Kautza M, Jonat W, Siebert R, Ammerpohl O. DNA-methylation profiling of fetal tissues reveals marked epigenetic differences between chorionic and amniotic samples. PLoS One 2012; 7:e39014. [PMID: 22723920 PMCID: PMC3378600 DOI: 10.1371/journal.pone.0039014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 05/15/2012] [Indexed: 12/24/2022] Open
Abstract
Epigenetic mechanisms including DNA methylation are supposed to play a key role in fetal development. Here we have investigated fetal DNA-methylation levels of 27,578 CpG loci in 47 chorionic villi (CVS) and 16 amniotic cell (AC) samples. Methylation levels differed significantly between karyotypically normal AC and CVS for 2,014 genes. AC showed more extreme DNA-methylation levels of these genes than CVS and the differentially methylated genes are significantly enriched for processes characteristic for the different cell types sampled. Furthermore, we identified 404 genes differentially methylated in CVS with trisomy 21. These genes were significantly enriched for high CG dinucleotid (CpG) content and developmental processes associated with Down syndrome. Our study points to major tissue-specific differences of fetal DNA-methylation and gives rise to the hypothesis that part of the Down syndrome phenotype is epigenetically programmed in the first trimester of pregnancy.
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Affiliation(s)
- Christel Eckmann-Scholz
- Department of Gynecology & Obstetrics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Susanne Bens
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sina Schneppenheim
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Almuth Caliebe
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Simone Heidemann
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Constantin von Kaisenberg
- Department of Gynecology & Obstetrics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
- Department of Obstetrics, Gynecology and Reproductive Medicine, Hannover Medical School, Hannover, Germany
| | | | - Walter Jonat
- Department of Gynecology & Obstetrics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
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18
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Zucchi FCR, Yao Y, Metz GA. The secret language of destiny: stress imprinting and transgenerational origins of disease. Front Genet 2012; 3:96. [PMID: 22675331 PMCID: PMC3366387 DOI: 10.3389/fgene.2012.00096] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 05/10/2012] [Indexed: 12/24/2022] Open
Abstract
Epigenetic regulation modulates gene expression without altering the DNA sequence to facilitate rapid adjustments to dynamically changing environmental conditions. The formation of an epigenetic memory allows passing on this information to subsequent generations. Here we propose that epigenetic memories formed by adverse environmental conditions and stress represent a critical determinant of health and disease in the F3 generation and beyond. Transgenerational programming of epigenetic regulation may represent a key to understand adult-onset complex disease pathogenesis and cumulative effects of life span and familial disease etiology. Ultimately, the mechanisms of generating an epigenetic memory may become of potentially promising diagnostic and therapeutic relevance due to their reversible nature. Exploring the role of environmental factors, such as stress, in causing variations in epigenetic profiles may lead to new avenues of personalized, preventive medicine based on epigenetic signatures and interventions.
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Affiliation(s)
- Fabiola C R Zucchi
- Canadian Centre for Behavioural Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
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19
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Abstract
The 15 years since the discovery of fetal DNA in maternal plasma have witnessed remarkable developments in noninvasive prenatal diagnosis. An understanding of biological parameters governing this phenomenon, such as the concentration and molecular size of circulating fetal DNA, has guided its diagnostic applications. Early efforts focused on the detection of paternally inherited sequences, which were absent in the maternal genome, in maternal plasma. Recent developments in precise measurement technologies such as digital polymerase chain reaction (PCR) have allowed the detection of minute allelic imbalances in plasma and have catalyzed analysis of single-gene disorders such as the hemoglobinopathies and hemophilia. The advent of massively parallel sequencing has enabled the robust detection of fetal trisomies in maternal plasma. Recent proof-of-concept studies have detected a chromosomal translocation and a microdeletion and have deduced a genome-wide genetic map of a fetus from maternal plasma. Understanding the ethical, legal, and social aspects in light of such rapid developments is thus a priority for future research.
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Affiliation(s)
- Yuk Ming Dennis Lo
- Li Ka Shing Institute of Health Sciences and Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
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20
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Bunce K, Chu T, Surti U, Hogge WA, Peters DG. Discovery of epigenetic biomarkers for the noninvasive diagnosis of fetal disease. Prenat Diagn 2012; 32:542-9. [PMID: 22495992 DOI: 10.1002/pd.3853] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/09/2012] [Accepted: 01/18/2012] [Indexed: 11/07/2022]
Abstract
OBJECTIVES The primary goal of this study was to identify CpG sites in the human genome that are differentially methylated in DNA obtained from chorionic villus sampling (CVS) samples and gestational age-matched maternal blood cell (MBC) samples. METHODS We used the HumanMethylation27 DNA Analysis BeadChip to characterize DNA methylation in samples of CVS and MBC. We then selected a subset of differentially methylated CpG sites on chromsome 13 and subjected them to analysis by mass spectrometry using the Epityper platform. RESULTS We identified 718 tissue-specific differentially methylated regions (DMRs) between MBC and CVS; 563 of these were hypermethylated in MBC and hypomethylated in CVS, whereas 155 sites were hypomethylated in MBC and hypermethylated in CVS. Further analysis of 13 DMRs on chromosome 13 by Epityper confirmed the microarray data and provided us with additional data about the methylation patterns of surrounding CpG sites. CONCLUSIONS Analysis of the resulting data identified a large number of cytosine-guanine dinucleotides that are potential biomarkers for the selective amplification of fetal DNA from maternal plasma and the subsequent noninvasive detection of trisomy 13.
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Affiliation(s)
- Kimberly Bunce
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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21
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Egger G, Wielscher M, Pulverer W, Kriegner A, Weinhäusel A. DNA methylation testing and marker validation using PCR: diagnostic applications. Expert Rev Mol Diagn 2012; 12:75-92. [PMID: 22133121 DOI: 10.1586/erm.11.90] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA methylation provides a fundamental epigenetic mechanism to establish and promote cell-specific gene-expression patterns, which are inherited by subsequent cell generations. Thus, the epigenome determines the differentiation into a cell lineage but can also program cells to become abnormal or malignant. In humans, different germline and somatic diseases have been linked to faulty DNA methylation. In this article, we will discuss the available PCR-based technologies to assess differences in DNA methylation levels mainly affecting 5-methylcytosine in the CpG dinucleotide context in hereditary syndromal and somatic pathological conditions. We will discuss some of the current diagnostic applications and provide an outlook on how DNA methylation-based biomarkers might provide novel tools for diagnosis, prognosis or patient stratification for diseases such as cancer.
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Affiliation(s)
- Gerda Egger
- Clinical Institute of Pathology, Medical University of Vienna, Austria
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22
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Zhang M, Li T, Chen J, Li L, Zhou C, Wang Y, Liu W, Zhang Y. Non-invasive prenatal diagnosis of trisomy 21 by dosage ratio of fetal chromosome-specific epigenetic markers in maternal plasma. JOURNAL OF HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY. MEDICAL SCIENCES = HUA ZHONG KE JI DA XUE XUE BAO. YI XUE YING DE WEN BAN = HUAZHONG KEJI DAXUE XUEBAO. YIXUE YINGDEWEN BAN 2011; 31:687. [PMID: 22038362 DOI: 10.1007/s11596-011-0583-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Indexed: 01/15/2023]
Abstract
This study examined the methylation difference in AIRE and RASSF1A between maternal and placental DNA, and the implication of this difference in the identification of free fetal DNA in maternal plasma and in prenatal diagnosis of trisomy 21. Maternal plasma samples were collected from 388 singleton pregnancies, and placental or chorionic villus tissues from 112 of them. Methylation-specific PCR (MSP) and methylation-sensitive restriction enzyme digestion followed by fluorescent quantitative PCR (MSRE + PCR) were employed to detect the maternal-fetal methylation difference in AIRE and RASSF1A. Diagnosis of trisomy 21 was established according to the ratio of fetal-specific AIRE to RASSF1A in maternal plasma. Both methods confirmed that AIRE and RASSF1A were hypomethylated in maternal blood cells but hypermethylated in placental or chorionic villus tissues. Moreover, the differential methylation for each locus could be seen during the whole pregnant period. The positive rates of fetal AIRE and RASSF1A in maternal plasma were found to be 78.1% and 82.1% by MSP and 94.8% and 96.9% by MSRE + PCR. MSRE + PCR was superior to MSP in the identification of fetal-specific hypermethylated sequences (P<0.05). Based on the data from 266 euploidy pregnancies, the 95% reference interval of the fetal AIRE/RASSF1A ratio in maternal plasma was 0.33-1.77, which was taken as the reference value for determining the numbers of fetal chromosome 21 in 102 pregnancies. The accuracy rate in 98 euploidy pregnancies was 96.9% (95/98). Three of the four trisomy 21 pregnancies were confirmed with this method. It was concluded that hypermethylated AIRE and RASSF1A may serve as fetal-specific markers for the identification of fetal DNA in maternal plasma and may be used for noninvasive prenatal diagnosis of trisomy 21.
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Affiliation(s)
- Ming Zhang
- Reproductive Medicine Center, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Tao Li
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jingyi Chen
- Reproductive Medicine Center, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Li Li
- Reproductive Medicine Center, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Chun Zhou
- Reproductive Medicine Center, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Yan Wang
- Reproductive Medicine Center, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Wenhui Liu
- Reproductive Medicine Center, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Yuanzhen Zhang
- Reproductive Medicine Center, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China.
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Hahn S, Lapaire O, Tercanli S, Kolla V, Hösli I. Determination of fetal chromosome aberrations from fetal DNA in maternal blood: has the challenge finally been met? Expert Rev Mol Med 2011; 13:e16. [PMID: 21542948 PMCID: PMC3087311 DOI: 10.1017/s1462399411001852] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The analysis of cell-free fetal nucleic acids in maternal blood for prenatal diagnosis has been transformed by several recent profound technology developments. The most noteworthy of these are 'digital PCR' and 'next-generation sequencing' (NGS), which might finally deliver the long-sought goal of noninvasive detection of fetal aneuploidy. Recent data, however, indicate that NGS might even be able to offer a much more detailed appraisal of the fetal genome, including paternal and maternal inheritance of point mutations for mendelian disorders such as β-thalassaemia. Although these developments are very exciting, in their current form they are still too complex and costly, and will need to be simplified considerably for their optimal translation to the clinic. In this regard, targeted NGS does appear to be a step in the right direction, although this should be seen in the context of ongoing progress with the isolation of fetal cells and with proteomic screening markers.
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Affiliation(s)
- Sinuhe Hahn
- Laboratory for Prenatal Medicine, Department of Biomedicine, University Hospital Basel, Switzerland.
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Pennings JLA, Rodenburg W, Imholz S, Koster MPH, van Oostrom CTM, Breit TM, Schielen PCJI, de Vries A. Gene expression profiling in a mouse model identifies fetal liver- and placenta-derived potential biomarkers for Down Syndrome screening. PLoS One 2011; 6:e18866. [PMID: 21533146 PMCID: PMC3077415 DOI: 10.1371/journal.pone.0018866] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 03/21/2011] [Indexed: 11/23/2022] Open
Abstract
Background As a first step to identify novel potential biomarkers for prenatal Down
Syndrome screening, we analyzed gene expression in embryos of wild type mice
and the Down Syndrome model Ts1Cje. Since current Down Syndrome screening
markers are derived from placenta and fetal liver, these tissues were chosen
as target. Methodology/Principal Findings Placenta and fetal liver at 15.5 days gestation were analyzed by microarray
profiling. We confirmed increased expression of genes located at the
trisomic chromosomal region. Overall, between the two genotypes more
differentially expressed genes were found in fetal liver than in placenta.
Furthermore, the fetal liver data are in line with the hematological
aberrations found in humans with Down Syndrome as well as Ts1Cje mice.
Together, we found 25 targets that are predicted (by Gene Ontology, UniProt,
or the Human Plasma Proteome project) to be detectable in human serum. Conclusions/Significance Fetal liver might harbor more promising targets for Down Syndrome screening
studies. We expect these new targets will help focus further experimental
studies on identifying and validating human maternal serum biomarkers for
Down Syndrome screening.
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Affiliation(s)
- Jeroen L A Pennings
- Laboratory for Health Protection Research (GBO), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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