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Nestor, Colm
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Publications (10 of 23) Show all publications
Thomson, J. P., Nestor, C. & Meehan, R. R. (2017). 5-Hydroxymethylcytosine Profiling in Human DNA. In: Paul Haggarty; Kristina Harrison (Ed.), Population Epigenetics: Methods and Protocols (pp. 89-98). Humana Press, 1589
Open this publication in new window or tab >>5-Hydroxymethylcytosine Profiling in Human DNA
2017 (English)In: Population Epigenetics: Methods and Protocols / [ed] Paul Haggarty; Kristina Harrison, Humana Press, 2017, Vol. 1589, p. 89-98Chapter in book (Refereed)
Abstract [en]

Since its "re-discovery" in 2009, there has been significant interest in defining the genome-wide distribution of DNA marked by 5-hydroxymethylation at cytosine bases (5hmC). In recent years, technological advances have resulted in a multitude of unique strategies to map 5hmC across the human genome. Here we discuss the wide range of approaches available to map this modification and describe in detail the affinity based methods which result in the enrichment of 5hmC marked DNA for downstream analysis.

Place, publisher, year, edition, pages
Humana Press, 2017
Series
Methods in Molecular Biology, ISSN 1064-3745, E-ISSN 1940-6029 ; 1589
Keywords
5-hydroxymethylcytosine; 5hmC; 5mC; DNA immunoprecipitation and enrichment; Epigenetics; HmeDIP
National Category
Genetics
Identifiers
urn:nbn:se:liu:diva-145072 (URN)10.1007/7651_2015_268 (DOI)26126447 (PubMedID)978-1-4939-6901-2 (ISBN)978-1-4939-6903-6 (ISBN)
Available from: 2018-02-08 Created: 2018-02-08 Last updated: 2018-02-09
Gustafsson, M., Gawel, D., Alfredsson, L., Baranzini, S., Bjorkander, J., Blomgran, R., . . . Benson, M. (2015). A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases. Science Translational Medicine, 7(313), Article ID 313ra178.
Open this publication in new window or tab >>A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases
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2015 (English)In: Science Translational Medicine, ISSN 1946-6234, E-ISSN 1946-6242, Vol. 7, no 313, article id 313ra178Article in journal (Refereed) Published
Abstract [en]

Early regulators of disease may increase understanding of disease mechanisms and serve as markers for presymptomatic diagnosis and treatment. However, early regulators are difficult to identify because patients generally present after they are symptomatic. We hypothesized that early regulators of T cell-associated diseases could be found by identifying upstream transcription factors (TFs) in T cell differentiation and by prioritizing hub TFs that were enriched for disease-associated polymorphisms. A gene regulatory network (GRN) was constructed by time series profiling of the transcriptomes and methylomes of human CD4(+) T cells during in vitro differentiation into four helper T cell lineages, in combination with sequence-based TF binding predictions. The TFs GATA3, MAF, and MYB were identified as early regulators and validated by ChIP-seq (chromatin immunoprecipitation sequencing) and small interfering RNA knockdowns. Differential mRNA expression of the TFs and their targets in T cell-associated diseases supports their clinical relevance. To directly test if the TFs were altered early in disease, T cells from patients with two T cell-mediated diseases, multiple sclerosis and seasonal allergic rhinitis, were analyzed. Strikingly, the TFs were differentially expressed during asymptomatic stages of both diseases, whereas their targets showed altered expression during symptomatic stages. This analytical strategy to identify early regulators of disease by combining GRNs with genome-wide association studies may be generally applicable for functional and clinical studies of early disease development.

Place, publisher, year, edition, pages
AMER ASSOC ADVANCEMENT SCIENCE, 2015
National Category
Biological Sciences Clinical Medicine
Identifiers
urn:nbn:se:liu:diva-123522 (URN)10.1126/scitranslmed.aad2722 (DOI)000365237400003 ()26560356 (PubMedID)
Note

Funding Agencies|Cancer fund, Swedish Medical Research Council [K2013-61X-22310-01-04, 2012-3168]; Academy of Finland Centre of Excellence in Molecular Systems Immunology and Physiology Research [250114]; Sigrid Juselius Foundation; Generalitat de Catalunya AGAUR [2014-SGR364]; Spanish Association Against Cancer; Spanish Ministry of Health ISCIII FIS [PI12/01528]; RTICC [RD12/0036/0008]

Available from: 2015-12-22 Created: 2015-12-21 Last updated: 2018-04-10Bibliographically approved
Nestor, C. E., Ottaviano, R., Reinhardt, D., Cruickshanks, H. A., Mjoseng, H. K., McPherson, R. C., . . . Meehan, R. R. (2015). Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems.. Genome Biology, 16, 11
Open this publication in new window or tab >>Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems.
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2015 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 16, p. 11-Article in journal (Refereed) Published
Abstract [en]

BackgroundThe DNA methylation profile of mammalian cell lines differs from the primary tissue from which they were derived, exhibiting increasing divergence from the in vivo methylation profile with extended time in culture. Few studies have directly examined the initial epigenetic and transcriptional consequences of adaptation of primary mammalian cells to culture, and the potential mechanisms through which this epigenetic dysregulation occurs is unknown.ResultsWe demonstrate that adaptation of mouse embryonic fibroblast, MEFS, to cell culture results in a rapid reprogramming of epigenetic and transcriptional states. We observed global 5-hydroxymethylcytosine (5hmC) erasure within three days of culture initiation. Loss of genic 5hmC was independent of global 5-methylcytosine (5mC) levels and could be partially rescued by addition of Vitamin C. Significantly, 5hmC loss was not linked to concomitant changes in transcription. Discrete promoter-specific gains of 5mC were also observed within seven days of culture initiation. Against this background of global 5hmC loss we identified a handful of developmentally important genes that maintained their 5hmC profile in culture, including the imprinted loci Gnas and H19. Similar outcomes were identified in the adaption of CD4+ T-cells to culture.ConclusionsWe report a dramatic and novel consequence of adaptation of mammalian cells to culture in which global loss of 5hmC occurs; suggesting rapid concomitant loss of methylcytosine dioxygenase activity. The observed epigenetic and transcriptional re-programming occurs much earlier than previously assumed, and has significant implications for the use of cell lines as faithful mimics of in vivo epigenetic and physiological processes.

Place, publisher, year, edition, pages
BioMed Central, 2015
National Category
Other Clinical Medicine
Identifiers
urn:nbn:se:liu:diva-115295 (URN)10.1186/s13059-014-0576-y (DOI)000351819300001 ()25648825 (PubMedID)
Note

We thank Professors Adrian Bird and Nicholas Hastie for their comments on our manuscript. JT and RO are funded by IMI-MARCAR (under grant agreement number (115001) (MARCAR project)). Work in RM's lab is supported by the MRC, IMI-MARCAR and the BBSRC. This work in RM's lab was also initially funded by the Breakthrough Breast Cancer charity. Work in MB's lab was supported by Linkoping University strategic research funding and the Ake Wibergs fund (3772738). Work in SP's lab is supported by the BBSRC.

Available from: 2015-03-12 Created: 2015-03-12 Last updated: 2017-12-04Bibliographically approved
Bruhn, S., Fang, Y., Barrenäs, F., Gustafsson, M., Zhang, H., Konstantinell, A., . . . Benson, M. (2014). A Generally Applicable Translational Strategy Identifies S100A4 as a Candidate Gene in Allergy. Science Translational Medicine, 6(218)
Open this publication in new window or tab >>A Generally Applicable Translational Strategy Identifies S100A4 as a Candidate Gene in Allergy
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2014 (English)In: Science Translational Medicine, ISSN 1946-6234, E-ISSN 1946-6242, Vol. 6, no 218Article in journal (Refereed) Published
Abstract [en]

The identification of diagnostic markers and therapeutic candidate genes in common diseases is complicated by the involvement of thousands of genes. We hypothesized that genes co-regulated with a key gene in allergy, IL13, would form a module that could help to identify candidate genes. We identified a T helper 2 (T(H)2) cell module by small interfering RNA-mediated knockdown of 25 putative IL13-regulating transcription factors followed by expression profiling. The module contained candidate genes whose diagnostic potential was supported by clinical studies. Functional studies of human TH2 cells as well as mouse models of allergy showed that deletion of one of the genes, S100A4, resulted in decreased signs of allergy including TH2 cell activation, humoral immunity, and infiltration of effector cells. Specifically, dendritic cells required S100A4 for activating T cells. Treatment with an anti-S100A4 antibody resulted in decreased signs of allergy in the mouse model as well as in allergen-challenged T cells from allergic patients. This strategy, which may be generally applicable to complex diseases, identified and validated an important diagnostic and therapeutic candidate gene in allergy.

Place, publisher, year, edition, pages
American Association for the Advancement of Science, 2014
National Category
Clinical Medicine Basic Medicine
Identifiers
urn:nbn:se:liu:diva-104118 (URN)10.1126/scitranslmed.3007410 (DOI)000329789600003 ()
Available from: 2014-02-07 Created: 2014-02-07 Last updated: 2018-01-11
Nestor, C., Barrenäs, F., Wang, H., Lentini, A., Zhang, H., Bruhn, S., . . . Benson, M. (2014). DNA Methylation Changes Separate Allergic Patients from Healthy Controls and May Reflect Altered CD4(+) T-Cell Population Structure. PLoS Genetics, 10(1), e1004059
Open this publication in new window or tab >>DNA Methylation Changes Separate Allergic Patients from Healthy Controls and May Reflect Altered CD4(+) T-Cell Population Structure
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2014 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 10, no 1, p. e1004059-Article in journal (Refereed) Published
Abstract [en]

Altered DNA methylation patterns in CD4(+) T-cells indicate the importance of epigenetic mechanisms in inflammatory diseases. However, the identification of these alterations is complicated by the heterogeneity of most inflammatory diseases. Seasonal allergic rhinitis (SAR) is an optimal disease model for the study of DNA methylation because of its welldefined phenotype and etiology. We generated genome-wide DNA methylation (N-patients = 8, N-controls = 8) and gene expression (N-patients = 9, N-controls = 10) profiles of CD4(+) T-cells from SAR patients and healthy controls using Illuminas HumanMethylation450 and HT-12 microarrays, respectively. DNA methylation profiles clearly and robustly distinguished SAR patients from controls, during and outside the pollen season. In agreement with previously published studies, gene expression profiles of the same samples failed to separate patients and controls. Separation by methylation (N-patients = 12, N-controls = 12), but not by gene expression (N-patients = 21, N-controls = 21) was also observed in an in vitro model system in which purified PBMCs from patients and healthy controls were challenged with allergen. We observed changes in the proportions of memory T-cell populations between patients (N-patients = 35) and controls (N-controls = 12), which could explain the observed difference in DNA methylation. Our data highlight the potential of epigenomics in the stratification of immune disease and represents the first successful molecular classification of SAR using CD4(+) T cells.

Place, publisher, year, edition, pages
Public Library of Science, 2014
National Category
Clinical Medicine Basic Medicine
Identifiers
urn:nbn:se:liu:diva-107871 (URN)10.1371/journal.pgen.1004059 (DOI)000336525000030 ()
Available from: 2014-06-23 Created: 2014-06-23 Last updated: 2019-02-11
Nestor, C. & Meehan, R. R. (2014). Hydroxymethylated DNA immunoprecipitation (hmeDIP). In: Juan C Stockert; Jesús Espada; Alfonso Blázquez-Castro (Ed.), Functional analysis of DNA and chromatin: (pp. 259-267). New York: Humana Press, 1094
Open this publication in new window or tab >>Hydroxymethylated DNA immunoprecipitation (hmeDIP)
2014 (English)In: Functional analysis of DNA and chromatin / [ed] Juan C Stockert; Jesús Espada; Alfonso Blázquez-Castro, New York: Humana Press, 2014, Vol. 1094, p. 259-267Chapter in book (Refereed)
Abstract [en]

5-hydroxymethylcytosine (5hmC) was recently identified as an abundant epigenetic mark in mammals. Subsequent research has implicated 5hmC in normal mammalian development and disease pathogenesis in humans. Many of the techniques commonly used to assay for canonical 5-methylcytosine (5mC) cannot distinguish between 5hmC and 5mC. The development of antibodies specific to 5hmC has allowed for specific enrichment of DNA fragments containing 5hmC. Hydroxymethylated DNA immunoprecipitation (hmeDIP) has become an invaluable tool for determining both locus-specific and genome-wide profiles of 5hmC in mammalian DNA. Here, we describe the use of hmeDIP to characterize the relative abundance of 5hmC at loci in mammalian DNA. 

Place, publisher, year, edition, pages
New York: Humana Press, 2014
Series
Methods in Molecular Biology, ISSN 1064-3745 ; vol 1094
Keywords
5-Hydroxymethylcytosine; Antibody; DNA; Hydroxymethylation; Immunoprecipitation; Methylation; Sonication
National Category
Clinical Medicine
Identifiers
urn:nbn:se:liu:diva-110532 (URN)10.1007/978-1-62703-706-8_20 (DOI)24162994 (PubMedID)2-s2.0-84891786709 (Scopus ID)978-1-62703-705-1 (ISBN)978-1-62703-706-8 (ISBN)
Note

Funding Agencies|MRC, Medical Research Council; BBSRC, Biotechnology and Biological Sciences Research Council

Available from: 2014-09-15 Created: 2014-09-12 Last updated: 2018-02-02Bibliographically approved
Gustafsson, M., Edström, M., Gawel, D., Nestor, C., Wang, H., Zhang, H., . . . Benson, M. (2014). Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment. Genome Medicine, 6(17)
Open this publication in new window or tab >>Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment
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2014 (English)In: Genome Medicine, ISSN 1756-994X, E-ISSN 1756-994X, Vol. 6, no 17Article in journal (Refereed) Published
Abstract [en]

Background: Translational research typically aims to identify and functionally validate individual, disease-specific genes. However, reaching this aim is complicated by the involvement of thousands of genes in common diseases, and that many of those genes are pleiotropic, that is, shared by several diseases. Methods: We integrated genomic meta-analyses with prospective clinical studies to systematically investigate the pathogenic, diagnostic and therapeutic roles of pleiotropic genes. In a novel approach, we first used pathway analysis of all published genome-wide association studies (GWAS) to find a cell type common to many diseases. Results: The analysis showed over-representation of the T helper cell differentiation pathway, which is expressed in T cells. This led us to focus on expression profiling of CD4(+) T cells from highly diverse inflammatory and malignant diseases. We found that pleiotropic genes were highly interconnected and formed a pleiotropic module, which was enriched for inflammatory, metabolic and proliferative pathways. The general relevance of this module was supported by highly significant enrichment of genetic variants identified by all GWAS and cancer studies, as well as known diagnostic and therapeutic targets. Prospective clinical studies of multiple sclerosis and allergy showed the importance of both pleiotropic and disease specific modules for clinical stratification. Conclusions: In summary, this translational genomics study identified a pleiotropic module, which has key pathogenic, diagnostic and therapeutic roles.

Place, publisher, year, edition, pages
BioMed Central, 2014
National Category
Clinical Medicine Basic Medicine
Identifiers
urn:nbn:se:liu:diva-106873 (URN)10.1186/gm534 (DOI)000334631300002 ()
Available from: 2014-05-28 Created: 2014-05-23 Last updated: 2018-04-10
Nestor, C. E., Reddington, J. P., Benson, M. & Meehan, R. R. (2014). Investigating 5-hydroxymethylcytosine (5hmC): the state of the art. Methods in Molecular Biology, 1094, 243-58
Open this publication in new window or tab >>Investigating 5-hydroxymethylcytosine (5hmC): the state of the art
2014 (English)In: Methods in Molecular Biology, ISSN 1064-3745, E-ISSN 1940-6029, Vol. 1094, p. 243-58Article in journal (Refereed) Published
Abstract [en]

The discovery of 5-hydroxymethylcytosine (5hmC) as an abundant base in mammalian genomes has excited the field of epigenetics, and stimulated an intense period of research activity aimed at decoding its biological significance. However, initial research efforts were hampered by a lack of assays capable of specifically detecting 5hmC. Consequently, the last 3 years have seen the development of a plethora of new techniques designed to detect both global levels and locus-specific profiles of 5hmC in mammalian genomes. This research effort has culminated in the recent publication of two complementary techniques for quantitative, base-resolution mapping of 5hmC in mammalian genomes, the first true mammalian hydroxymethylomes. Here, we review the techniques currently available to researchers studying 5hmC, discuss their advantages and disadvantages, and explore the technical hurdles which remain to be overcome.

Place, publisher, year, edition, pages
Humana Press, 2014
National Category
Basic Medicine
Identifiers
urn:nbn:se:liu:diva-109427 (URN)10.1007/978-1-62703-706-8_19 (DOI)24162993 (PubMedID)
Available from: 2014-08-18 Created: 2014-08-18 Last updated: 2018-01-11Bibliographically approved
Gustafsson, M., Nestor, C., Zhang, H., Barabasi, A.-L., Baranzini, S., Brunak, S., . . . Benson, M. (2014). Modules, networks and systems medicine for understanding disease and aiding diagnosis. Genome Medicine, 6(82)
Open this publication in new window or tab >>Modules, networks and systems medicine for understanding disease and aiding diagnosis
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2014 (English)In: Genome Medicine, ISSN 1756-994X, E-ISSN 1756-994X, Vol. 6, no 82Article, review/survey (Refereed) Published
Abstract [en]

Many common diseases, such as asthma, diabetes or obesity, involve altered interactions between thousands of genes. High-throughput techniques (omics) allow identification of such genes and their products, but functional understanding is a formidable challenge. Network-based analyses of omics data have identified modules of disease-associated genes that have been used to obtain both a systems level and a molecular understanding of disease mechanisms. For example, in allergy a module was used to find a novel candidate gene that was validated by functional and clinical studies. Such analyses play important roles in systems medicine. This is an emerging discipline that aims to gain a translational understanding of the complex mechanisms underlying common diseases. In this review, we will explain and provide examples of how network-based analyses of omics data, in combination with functional and clinical studies, are aiding our understanding of disease, as well as helping to prioritize diagnostic markers or therapeutic candidate genes. Such analyses involve significant problems and limitations, which will be discussed. We also highlight the steps needed for clinical implementation.

Place, publisher, year, edition, pages
BioMed Central, 2014
National Category
Clinical Medicine
Identifiers
urn:nbn:se:liu:diva-112648 (URN)10.1186/s13073-014-0082-6 (DOI)000344570000001 ()25473422 (PubMedID)
Note

Funding Agencies|European Commission under the Seventh Framework Programme, CASyM; Swedish Medical Research Council; Linkoping University

Available from: 2014-12-05 Created: 2014-12-05 Last updated: 2017-12-05
Nestor, C. E., Dadfa, E., Ernerudh, J., Gustafsson, M., Björkander, J. F., Benson, M. & Zhang, H. (2014). Sublingual immunotherapy alters expression of IL-4 and its soluble and membrane-bound receptors. Allergy. European Journal of Allergy and Clinical Immunology, 69(11), 1564-1566
Open this publication in new window or tab >>Sublingual immunotherapy alters expression of IL-4 and its soluble and membrane-bound receptors
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2014 (English)In: Allergy. European Journal of Allergy and Clinical Immunology, ISSN 0105-4538, E-ISSN 1398-9995, Vol. 69, no 11, p. 1564-1566Article in journal (Refereed) Published
Abstract [en]

Seasonal allergic rhinitis (SAR) is a disease of increasing prevalence, which results from an inappropriate T-helper cell, type 2 (Th2) response to pollen. Specific immunotherapy (SIT) involves repeated treatment with small doses of pollen and can result in complete and lasting reversal of SAR. Here, we assayed the key Th2 cytokine, IL-4, and its soluble and membrane-bound receptor in SAR patients before and after SIT. Using allergen-challenge assays, we found that SIT treatment decreased IL-4 cytokine levels, as previously reported. We also observed a significant decrease in the IL-4 membrane-bound receptor (mIL4R) at both the level of mRNA and protein. SIT treatment resulted in a significant increase in the inhibitory soluble IL-4 receptor (sIL4R). Reciprocal changes in mIL4R and sIL4R were also observed in patient serum. Altered mIL4R and sIL4R is a novel explanation for the positive effects of immunotherapy with potential basic and clinical research implications.

Place, publisher, year, edition, pages
Wiley, 2014
National Category
Clinical Medicine Basic Medicine
Identifiers
urn:nbn:se:liu:diva-109429 (URN)10.1111/all.12505 (DOI)000343851200016 ()25130266 (PubMedID)
Available from: 2014-08-18 Created: 2014-08-18 Last updated: 2018-01-11
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