1
|
Abstract
Precision medicine relies on validated biomarkers with which to better classify patients by their probable disease risk, prognosis and/or response to treatment. Although affordable 'omics'-based technology has enabled faster identification of putative biomarkers, the validation of biomarkers is still stymied by low statistical power and poor reproducibility of results. This Review summarizes the successes and challenges of using different types of molecule as biomarkers, using lung cancer as a key illustrative example. Efforts at the national level of several countries to tie molecular measurement of samples to patient data via electronic medical records are the future of precision medicine research.
Collapse
Affiliation(s)
- Ashley J Vargas
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Room 3068A, MSC 425, 837 Convent Drive, Bethesda, Maryland 20892-4258, USA
- Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland 20850, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Room 3068A, MSC 425, 837 Convent Drive, Bethesda, Maryland 20892-4258, USA
| |
Collapse
|
2
|
DNA Methylation Profiling Reveals Correlation of Differential Methylation Patterns with Gene Expression in Human Epilepsy. J Mol Neurosci 2016; 59:68-77. [DOI: 10.1007/s12031-016-0735-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/04/2016] [Indexed: 12/11/2022]
|
3
|
Pandey RV, Pulverer W, Walter P, Kallmeyer R, Beikircher G, Pabinger S, Kriegner A, Weinhäusel A. MSRE-HTPrimer: a high-throughput and genome-wide primer design pipeline optimized for epigenetic research. Clin Epigenetics 2016; 8:26. [PMID: 26949424 PMCID: PMC4779238 DOI: 10.1186/s13148-016-0190-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 02/23/2016] [Indexed: 12/28/2022] Open
Abstract
Background Methylation-sensitive restriction enzymes—polymerase chain reaction (MSRE-PCR) has been used in epigenetic research to identify genome-wide and gene-specific DNA methylation. Currently, epigenome-wide discovery studies provide many candidate regions for which the MSREqPCR approach can be very effective to confirm the findings. MSREqPCR provides high multiplexing capabilities also when starting with limited amount of DNA-like cfDNA to validate many targets in a time- and cost-effective manner. Multiplex design is challenging and cumbersome to define specific primers in an effective manner, and no suitable software tools are freely available for high-throughput primer design in a time-effective manner and to automatically annotate the resulting primers with known SNPs, CpG, repeats, and RefSeq genes. Therefore a robust, powerful, high-throughput, optimized, and methylation-specific primer design tool with great accuracy will be very useful. Results We have developed a novel pipeline, called MSRE-HTPrimer, to design MSRE-PCR and genomic PCR primers pairs in a very efficient manner and with high success rate. First, our pipeline designs all possible PCR primer pairs and oligos, followed by filtering for SNPs loci and repeat regions. Next, each primer pair is annotated with the number of cut sites in primers and amplicons, upstream and downstream genes, and CpG islands loci. Finally, MSRE-HTPrimer selects resulting primer pairs for all target sequences based on a custom quality matrix defined by the user. MSRE-HTPrimer produces a table for all resulting primer pairs as well as a custom track in GTF file format for each target sequence to visualize it in UCSC genome browser. Conclusions MSRE-HTPrimer, based on Primer3, is a high-throughput pipeline and has no limitation on the number and size of target sequences for primer design and provides full flexibility to customize it for specific requirements. It is a standalone web-based pipeline, which is fully configured within a virtual machine and thus can be readily used without any configuration. We have experimentally validated primer pairs designed by our pipeline and shown a very high success rate of primer pairs: out of 190 primer pairs, 71 % could be successfully validated. The MSRE-HTPrimer software is freely available from http://sourceforge.net/p/msrehtprimer/wiki/Virtual_Machine/ as a virtual machine. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0190-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ram Vinay Pandey
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria ; Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Walter Pulverer
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | | | - Rainer Kallmeyer
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | - Gabriel Beikircher
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | - Stephan Pabinger
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | - Albert Kriegner
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | - Andreas Weinhäusel
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| |
Collapse
|
4
|
Gupta R, Reifenberger RG, Kulkarni GU. Cellphone camera imaging of a periodically patterned chip as a potential method for point-of-care diagnostics. ACS APPLIED MATERIALS & INTERFACES 2014; 6:3923-3929. [PMID: 24564576 DOI: 10.1021/am4050426] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this study, we demonstrate that a disposable chip periodically patterned with suitable ligands, an ordinary cellphone camera, and a simple pattern recognition software, can potentially be used for quantitative diagnostics. A key factor in this demonstration is the design of a calibration grid around the chip that, through a contrast transfer process, enables reliable analysis of the images collected under variable ambient lighting conditions. After exposure to a dispersion of amine terminated silica beads used as analyte mimicking pathogens, an epoxy-terminated glass substrate microcontact printed with octadecyltrichlorosilane (250 μm periodicity) developed a characteristic pattern of beads which could be easily imaged with a cellphone camera of 3.2 MP pixels. A simple pattern recognition algorithm using fast Fourier transform produced a quantitative estimate of the analyte concentration present in the test solution. In this method importantly, neither the chip fabrication process nor the fill-factor of the periodic pattern need be perfect to arrive at a conclusive diagnosis. The method suggests a viable platform that may potentially find use in fault-tolerant and robust point-of-care diagnostic applications.
Collapse
Affiliation(s)
- Ritu Gupta
- Chemistry and Physics of Materials Unit, DST Unit on Nanoscience, Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur P.O., Bangalore, Karnataka 560064, India
| | | | | |
Collapse
|
5
|
Liloglou T, Bediaga NG, Brown BR, Field JK, Davies MP. Epigenetic biomarkers in lung cancer. Cancer Lett 2014; 342:200-12. [DOI: 10.1016/j.canlet.2012.04.018] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 04/18/2012] [Accepted: 04/22/2012] [Indexed: 12/31/2022]
|
6
|
Gao T, Nie Y, Guo J. Hypermethylation of the gene LARP2 for noninvasive prenatal diagnosis of β-thalassemia based on DNA methylation profile. Mol Biol Rep 2012; 39:6591-8. [PMID: 22327645 DOI: 10.1007/s11033-012-1489-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 01/24/2012] [Indexed: 12/31/2022]
Abstract
In order to identify epigenetic markers of β-thalassemia, a genome-wide profiling method named differential methylation hybridization was used to search these differentially methylated genes. Unsupervised hierarchical clustering and molecular annotation system were used to analyze the data, and methylation-specific PCR and real-time PCR were used to confirm the differentially methylated genes. This system was validated by detecting 13 cases, 10 of which were homo-zygous β-thalassaemia. Totally 113 genes were identified as methlyation-enriched genes (ratio ≥ 2.0, P < 0.05) and 96 genes were identified as hypomethylated genes in both groups (ratio ≤ 0.5, P < 0.05). The promoter of the gene of La ribonucleoprotein domain family (LARP2) was significantly hypermethylated in β-thalassemia, and the expression of LARP2 was significantly lower in β-thalassemia. Hypermethylation of the LARP2 promoter was correlated with its lower expression in β-thalassemia and our chip-based DNA methylation detection system can provide earlier diagnosis of β-thalassemia using this epigenetic marker.
Collapse
Affiliation(s)
- Tian Gao
- Department of Gynecology and Obstetrics, The First Affiliated Hospital, Chongqiang Medical University, Chongqing, China
| | | | | |
Collapse
|
7
|
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.
Collapse
Affiliation(s)
- Gerda Egger
- Clinical Institute of Pathology, Medical University of Vienna, Austria
| | | | | | | | | |
Collapse
|
8
|
Li CCY, Cropley JE, Cowley MJ, Preiss T, Martin DIK, Suter CM. A sustained dietary change increases epigenetic variation in isogenic mice. PLoS Genet 2011; 7:e1001380. [PMID: 21541011 PMCID: PMC3080854 DOI: 10.1371/journal.pgen.1001380] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 03/21/2011] [Indexed: 02/07/2023] Open
Abstract
Epigenetic changes can be induced by adverse environmental exposures, such as
nutritional imbalance, but little is known about the nature or extent of these
changes. Here we have explored the epigenomic effects of a sustained nutritional
change, excess dietary methyl donors, by assessing genomic CpG methylation
patterns in isogenic mice exposed for one or six generations. We find stochastic
variation in methylation levels at many loci; exposure to methyl donors
increases the magnitude of this variation and the number of variable loci.
Several gene ontology categories are significantly overrepresented in genes
proximal to these methylation-variable loci, suggesting that certain pathways
are susceptible to environmental influence on their epigenetic states. Long-term
exposure to the diet (six generations) results in a larger number of loci
exhibiting epigenetic variability, suggesting that some of the induced changes
are heritable. This finding presents the possibility that epigenetic variation
within populations can be induced by environmental change, providing a vehicle
for disease predisposition and possibly a substrate for natural selection. Epigenetic changes to gene expression that do not involve changes to DNA sequence
can be influenced by the environment and provide one candidate mechanism by
which early nutrition can influence adult disease risk. Here, we examined
epigenetic changes across the genome in response to short- and long-term
exposure to a dietary supplement in genetically identical mice. We find that the
supplement induces small but widespread epigenetic changes in exposed mice.
These changes increase the epigenetic variability among exposed mice, and this
effect is magnified in mice exposed long-term. The epigenetic changes are
overrepresented in gene functions involved in cell and organ development and in
gene expression. Our data is consistent with the external environment having
pervasive effects on the epigenome and suggests that some genetic pathways may
be more susceptible to environmental influence than others.
Collapse
Affiliation(s)
- Cheryl C. Y. Li
- Victor Chang Cardiac Research Institute,
University of New South Wales, Sydney, Australia
- Faculty of Medicine, University of New South
Wales, Sydney, Australia
| | - Jennifer E. Cropley
- Victor Chang Cardiac Research Institute,
University of New South Wales, Sydney, Australia
- Faculty of Medicine, University of New South
Wales, Sydney, Australia
| | - Mark J. Cowley
- Peter Wills Bioinformatics Centre, Garvan
Institute of Medical Research, Sydney, Australia
- Cancer Research Program, Garvan Institute of
Medical Research, Sydney, Australia
| | - Thomas Preiss
- Victor Chang Cardiac Research Institute,
University of New South Wales, Sydney, Australia
- Faculty of Medicine, University of New South
Wales, Sydney, Australia
- Faculty of Science, University of New South
Wales, Sydney, Australia
| | - David I. K. Martin
- Children's Hospital Oakland Research
Institute, Oakland, California, United States of America
| | - Catherine M. Suter
- Victor Chang Cardiac Research Institute,
University of New South Wales, Sydney, Australia
- Faculty of Medicine, University of New South
Wales, Sydney, Australia
- * E-mail:
| |
Collapse
|
9
|
Qureshi SA, Bashir MU, Yaqinuddin A. Utility of DNA methylation markers for diagnosing cancer. Int J Surg 2010; 8:194-8. [PMID: 20139036 DOI: 10.1016/j.ijsu.2010.02.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 01/21/2010] [Accepted: 02/02/2010] [Indexed: 01/07/2023]
Abstract
DNA methylation occurs at the CpG residues and serves as a powerful epigenetic mechanism that negatively regulates gene expression. This process is catalyzed by DNA methyltransferases and occurs within "CpG islands" found in the promoter regions of >70% of human genes. Given the important role of DNA methylation in regulating gene expression, un-programmed changes in methylation patterns are expected to either silence or activate transcription of tumor suppressor genes (via hypermethylation) or oncogenes (via demethylation), respectively, and by doing so promote a disease state. In light of the fact that a number of different cancers are frequently associated with hypermethylated tumor suppressor genes together with the observation that tumor derived genomic DNAs are present in various body fluids including serum/plasma, urine, sputum and bronchial lavage, methylated DNA has shown tremendous promise to serve as a robust biomarker for detecting cancer. Over the last several years protocols for capturing small amounts of DNA in circulation have been developed. Once captured, DNA methylation may be readily monitored by restriction enzyme digestion or bisulfite conversion followed by amplification of the desired genomic region with the polymerase chain reaction (PCR). New technologies which employ methyl-binding protein or antibodies that bind specifically to methylated-CpG residues have now enabled investigators to interrogate the status of entire "DNA methyome" of diseased tissue in an efficient and cost-effective manner. In this review, we describe the various tumor suppressor genes that are frequently hypermethylated in different cancers and how these and other methylated loci may be employed as clinically useful biomarkers for diagnosing cancer noninvasively using readily available body fluids.
Collapse
Affiliation(s)
- Sohail A Qureshi
- Department of Biological and Biomedical Sciences, and Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan.
| | | | | |
Collapse
|
10
|
|
11
|
Abstract
Clinical signs and symptoms, as well as medical and dental history, are all considered in the clinical determination of gingival inflammation and periodontal disease severity. However, the "biologic systems model" highlights that the clinical presentation of periodontal disease is closely tied to the underlying biologic phenotype. We propose that the determination and integration of subject-level factors, microbial composition, systemic immune response, and gingival tissue inflammatory mediator responses will better reflect the biology of the biofilm-gingival interface in a specific patient and may provide insights on clinical management. Disease classifications and multivariable models further refine the biologic basis for the increasing severity of periodontal disease expression. As such, new classifications may better identify disease-susceptible and treatment-non-responsive individuals than current classifications that are heavily influenced by probing and attachment level measurements alone. New data also suggest that the clinical characteristics of some complex diseases, such as periodontal disease, are influenced by the genetic and epigenetic contributions to clinical phenotype. Although the genetic basis for periodontal disease is considered imperative for setting an inflammatory capacity for an individual and, thus, a threshold for severity, there is evidence to suggest an epigenetic component is involved as well. Many factors long associated with periodontitis, including bacterial accumulations, smoking, and diabetes, are known to produce strong epigenetic changes in tissue behavior. We propose that we are now able to rethink periodontal disease in terms of a biologic systems model that may help to establish more homogeneous diagnostic categories and can provide insight into the expected response to treatment.
Collapse
Affiliation(s)
- Steven Offenbacher
- Center for Oral and Systemic Disease, Department of Periodontology, University of North Carolina at Chapel Hill, Manning Drive and Columbia Street, Chapel Hill, NC 27599, USA.
| | | | | |
Collapse
|