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van der Zwan YG, Rijlaarsdam MA, Rossello FJ, Notini AJ, de Boer S, Watkins DN, Gillis AJM, Dorssers LCJ, White SJ, Looijenga LHJ. Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines. PLoS One 2014; 9:e98330. [PMID: 24887064 PMCID: PMC4041891 DOI: 10.1371/journal.pone.0098330] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 04/30/2014] [Indexed: 12/12/2022] Open
Abstract
Background Originating from Primordial Germ Cells/gonocytes and developing via a precursor lesion called Carcinoma In Situ (CIS), Germ Cell Cancers (GCC) are the most common cancer in young men, subdivided in seminoma (SE) and non-seminoma (NS). During physiological germ cell formation/maturation, epigenetic processes guard homeostasis by regulating the accessibility of the DNA to facilitate transcription. Epigenetic deregulation through genetic and environmental parameters (i.e. genvironment) could disrupt embryonic germ cell development, resulting in delayed or blocked maturation. This potentially facilitates the formation of CIS and progression to invasive GCC. Therefore, determining the epigenetic and functional genomic landscape in GCC cell lines could provide insight into the pathophysiology and etiology of GCC and provide guidance for targeted functional experiments. Results This study aims at identifying epigenetic footprints in SE and EC cell lines in genome-wide profiles by studying the interaction between gene expression, DNA CpG methylation and histone modifications, and their function in the pathophysiology and etiology of GCC. Two well characterized GCC-derived cell lines were compared, one representative for SE (TCam-2) and the other for EC (NCCIT). Data were acquired using the Illumina HumanHT-12-v4 (gene expression) and HumanMethylation450 BeadChip (methylation) microarrays as well as ChIP-sequencing (activating histone modifications (H3K4me3, H3K27ac)). Results indicate known germ cell markers not only to be differentiating between SE and NS at the expression level, but also in the epigenetic landscape. Conclusion The overall similarity between TCam-2/NCCIT support an erased embryonic germ cell arrested in early gonadal development as common cell of origin although the exact developmental stage from which the tumor cells are derived might differ. Indeed, subtle difference in the (integrated) epigenetic and expression profiles indicate TCam-2 to exhibit a more germ cell-like profile, whereas NCCIT shows a more pluripotent phenotype. The results provide insight into the functional genome in GCC cell lines.
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Affiliation(s)
- Yvonne G. van der Zwan
- Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martin A. Rijlaarsdam
- Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Fernando J. Rossello
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - Amanda J. Notini
- Centre for Genetic Diseases, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - Suzan de Boer
- Centre for Genetic Diseases, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - D. Neil Watkins
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - Ad J. M. Gillis
- Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lambert C. J. Dorssers
- Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Stefan J. White
- Centre for Genetic Diseases, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - Leendert H. J. Looijenga
- Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
- * E-mail:
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Rapid and unambiguous detection of DNase I hypersensitive site in rare population of cells. PLoS One 2014; 9:e85740. [PMID: 24465674 PMCID: PMC3897510 DOI: 10.1371/journal.pone.0085740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 12/02/2013] [Indexed: 11/19/2022] Open
Abstract
DNase I hypersensitive (DHS) sites are important for understanding cis regulation of gene expression. However, existing methods for detecting DHS sites in small numbers of cells can lead to ambiguous results. Here we describe a simple new method, in which DNA fragments with ends generated by DNase I digestion are isolated and used as templates for two PCR reactions. In the first PCR, primers are derived from sequences up- and down-stream of the DHS site. If the DHS site exists in the cells, the first PCR will not produce PCR products due to the cuts of the templates by DNase I between the primer sequences. In the second PCR, one primer is derived from sequence outside the DHS site and the other from the adaptor. This will produce a smear of PCR products of different sizes due to cuts by DNase I at different positions at the DHS site. With this design, we detected a DHS site at the CD4 gene in two CD4 T cell populations using as few as 2×10(4) cells. We further validated this method by detecting a DHS site of the IL-4 gene that is specifically present in type 2 but not type 1 T helper cells. Overall, this method overcomes the interference by genomic DNA not cut by DNase I at the DHS site, thereby offering unambiguous detection of DHS sites in the cells.
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Abstract
DNaseI-hypersensitive sites within chromatin are indicative of genomic loci with regulatory function. Several techniques have been described for analyzing these regions, but are either laborious, offer low-throughput possibilities, or are expensive. We have developed a new approach based on a modified version of multiplex ligation-dependent probe amplification (MLPA). Using this method, it is possible to analyse up to 50 defined genomic regions for DNaseI-hypersensitivity in a single PCR-based reaction. This chapter outlines the approach and discusses the critical features of each step of the procedure.
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Affiliation(s)
- Thomas Ohnesorg
- Molecular Development Laboratory, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
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White S, Ohnesorg T, Notini A, Roeszler K, Hewitt J, Daggag H, Smith C, Turbitt E, Gustin S, van den Bergen J, Miles D, Western P, Arboleda V, Schumacher V, Gordon L, Bell K, Bengtsson H, Speed T, Hutson J, Warne G, Harley V, Koopman P, Vilain E, Sinclair A. Copy number variation in patients with disorders of sex development due to 46,XY gonadal dysgenesis. PLoS One 2011; 6:e17793. [PMID: 21408189 PMCID: PMC3049794 DOI: 10.1371/journal.pone.0017793] [Citation(s) in RCA: 94] [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: 10/27/2010] [Accepted: 02/14/2011] [Indexed: 01/07/2023] Open
Abstract
Disorders of sex development (DSD), ranging in severity from mild genital abnormalities to complete sex reversal, represent a major concern for patients and their families. DSD are often due to disruption of the genetic programs that regulate gonad development. Although some genes have been identified in these developmental pathways, the causative mutations have not been identified in more than 50% 46,XY DSD cases. We used the Affymetrix Genome-Wide Human SNP Array 6.0 to analyse copy number variation in 23 individuals with unexplained 46,XY DSD due to gonadal dysgenesis (GD). Here we describe three discrete changes in copy number that are the likely cause of the GD. Firstly, we identified a large duplication on the X chromosome that included DAX1 (NR0B1). Secondly, we identified a rearrangement that appears to affect a novel gonad-specific regulatory region in a known testis gene, SOX9. Surprisingly this patient lacked any signs of campomelic dysplasia, suggesting that the deletion affected expression of SOX9 only in the gonad. Functional analysis of potential SRY binding sites within this deleted region identified five putative enhancers, suggesting that sequences additional to the known SRY-binding TES enhancer influence human testis-specific SOX9 expression. Thirdly, we identified a small deletion immediately downstream of GATA4, supporting a role for GATA4 in gonad development in humans. These CNV analyses give new insights into the pathways involved in human gonad development and dysfunction, and suggest that rearrangements of non-coding sequences disturbing gene regulation may account for significant proportion of DSD cases.
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Affiliation(s)
- Stefan White
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas Ohnesorg
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Amanda Notini
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Kelly Roeszler
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Jacqueline Hewitt
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Hinda Daggag
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Craig Smith
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Erin Turbitt
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Sonja Gustin
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Jocelyn van den Bergen
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Denise Miles
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Patrick Western
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Valerie Arboleda
- Department of Medical Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Valerie Schumacher
- Pediatrics Department, Children's Hospital, Boston, Massachusetts, United States of America
| | - Lavinia Gordon
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Katrina Bell
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | | | - Terry Speed
- Walter and Eliza Hall Institute, Melbourne, Victoria, Australia
| | - John Hutson
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Garry Warne
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Vincent Harley
- Prince Henry's Institute of Medical Research, Melbourne, Victoria, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Eric Vilain
- Department of Medical Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Andrew Sinclair
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
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Abstract
Multiplex Ligation-dependent Probe Amplification (MLPA) is a PCR-based technique that was developed for identifying deletions and duplications in genomic DNA. The simplicity and sensitivity of this approach has led to it being implemented in many laboratories around the world. Since the original publication, there have been several variants of MLPA described, allowing the quantitative analysis of mRNA transcript levels, CpG methylation, complex genomic regions, and DNaseI hypersensitive sites. This chapter outlines the basic MLPA protocol, describes the different modifications and applications that have been published, and discusses the critical points during each of the steps.
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Affiliation(s)
- Thomas Ohnesorg
- Molecular Development, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
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Rooms L, Vandeweyer G, Reyniers E, van Mol K, de Canck I, Van der Aa N, Rossau R, Kooy RF. Array-based MLPA to detect recurrent copy number variations in patients with idiopathic mental retardation. Am J Med Genet A 2011; 155A:343-8. [PMID: 21271651 DOI: 10.1002/ajmg.a.33810] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 10/03/2010] [Indexed: 02/04/2023]
Abstract
Microdeletions, either subtelomeric or interstitial, are responsible for the mental handicap in approximately 10-20% of all patients. Currently, Multiplex Ligation-dependent Probe Amplification (MLPA) is widely used to detect these small aberrations in a routine fashion. Although cost-effective, the throughput is low and the degree of multiplexing is limited to maximally 40-50 probes. Therefore, we developed an array-based MLPA method, with probes identified by unique tag sequences, allowing the simultaneous analysis of 180 probes in a single experiment thereby covering all known mental retardation loci with at least two probes. We screened 120 patients with idiopathic mental retardation. In this group we detected 6 aberrations giving a detection rate of 5%, consistent with similar studies. In addition we tested 293 patients with mental retardation who were negative for fragile X syndrome and commercially available subtelomeric MLPA. We found seven causative rearrangements in this group (detection rate of 2.4%) thereby illustrating the value of including probes for interstitial microdeletion syndromes and additional probes in the telomeric regions in targeted screening sets for mental retardation. Array-based MLPA may thus be a good candidate to develop probe sets that rapidly detect copy number changes of disease associated loci in the human genome. This method may become a valuable tool in a routine diagnostic setting as it is a fast, user-friendly and relatively low-cost technique providing straightforward results requiring only 125 ng of genomic DNA.
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Affiliation(s)
- Liesbeth Rooms
- Department of Medical Genetics, University of Antwerp and University Hospital, Antwerp, Belgium
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Marcinkowska M, Wong KK, Kwiatkowski DJ, Kozlowski P. Design and generation of MLPA probe sets for combined copy number and small-mutation analysis of human genes: EGFR as an example. ScientificWorldJournal 2010; 10:2003-18. [PMID: 20953551 PMCID: PMC4004796 DOI: 10.1100/tsw.2010.195] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Multiplex ligation-dependent probe amplification (MLPA) is a multiplex copy number analysis method that is routinely used to identify large mutations in many clinical and research labs. One of the most important drawbacks of the standard MLPA setup is a complicated, and therefore expensive, procedure of generating long MLPA probes. This drawback substantially limits the applicability of MLPA to those genomic regions for which ready-to-use commercial kits are available. Here we present a simple protocol for designing MLPA probe sets that are composed entirely of short oligonucleotide half-probes generated through chemical synthesis. As an example, we present the design and generation of an MLPA assay for parallel copy number and small-mutation analysis of the EGFR gene.
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Affiliation(s)
- Malgorzata Marcinkowska
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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