1
|
Utility of Lymphoblastoid Cell Lines for Induced Pluripotent Stem Cell Generation. Stem Cells Int 2016; 2016:2349261. [PMID: 27375745 PMCID: PMC4914736 DOI: 10.1155/2016/2349261] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/01/2016] [Accepted: 05/08/2016] [Indexed: 12/15/2022] Open
Abstract
A large number of EBV immortalized LCLs have been generated and maintained in genetic/epidemiological studies as a perpetual source of DNA and as a surrogate in vitro cell model. Recent successes in reprograming LCLs into iPSCs have paved the way for generating more relevant in vitro disease models using this existing bioresource. However, the overall reprogramming efficiency and success rate remain poor and very little is known about the mechanistic changes that take place at the transcriptome and cellular functional level during LCL-to-iPSC reprogramming. Here, we report a new optimized LCL-to-iPSC reprogramming protocol using episomal plasmids encoding pluripotency transcription factors and mouse p53DD (p53 carboxy-terminal dominant-negative fragment) and commercially available reprogramming media. We achieved a consistently high reprogramming efficiency and 100% success rate using this optimized protocol. Further, we investigated the transcriptional changes in mRNA and miRNA levels, using FC-abs ≥ 2.0 and FDR ≤ 0.05 cutoffs; 5,228 mRNAs and 77 miRNAs were differentially expressed during LCL-to-iPSC reprogramming. The functional enrichment analysis of the upregulated genes and activation of human pluripotency pathways in the reprogrammed iPSCs showed that the generated iPSCs possess transcriptional and functional profiles very similar to those of human ESCs.
Collapse
|
2
|
Zhou X, Cain CE, Myrthil M, Lewellen N, Michelini K, Davenport ER, Stephens M, Pritchard JK, Gilad Y. Epigenetic modifications are associated with inter-species gene expression variation in primates. Genome Biol 2015; 15:547. [PMID: 25468404 PMCID: PMC4290387 DOI: 10.1186/s13059-014-0547-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Changes in gene regulation have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels, yet we know much less about the extent to which regulatory mechanisms differ between species. RESULTS To begin addressing this gap, we perform a comparative epigenetic study in primate lymphoblastoid cell lines, to query the contribution of RNA polymerase II and four histone modifications, H3K4me1, H3K4me3, H3K27ac, and H3K27me3, to inter-species variation in gene expression levels. We find that inter-species differences in mark enrichment near transcription start sites are significantly more often associated with inter-species differences in the corresponding gene expression level than expected by chance alone. Interestingly, we also find that first-order interactions among the five marks, as well as chromatin states, do not markedly contribute to the degree of association between the marks and inter-species variation in gene expression levels, suggesting that the marginal effects of the five marks dominate this contribution. CONCLUSIONS Our observations suggest that epigenetic modifications are substantially associated with changes in gene expression levels among primates and may represent important molecular mechanisms in primate evolution.
Collapse
|
3
|
Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, Gilad Y. Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature. PLoS Genet 2015; 11:e1005216. [PMID: 25950834 PMCID: PMC4423863 DOI: 10.1371/journal.pgen.1005216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/13/2015] [Indexed: 11/18/2022] Open
Abstract
Renewable in vitro cell cultures, such as lymphoblastoid cell lines (LCLs), have facilitated studies that contributed to our understanding of genetic influence on human traits. However, the degree to which cell lines faithfully maintain differences in donor-specific phenotypes is still debated. We have previously reported that standard cell line maintenance practice results in a loss of donor-specific gene expression signatures in LCLs. An alternative to the LCL model is the induced pluripotent stem cell (iPSC) system, which carries the potential to model tissue-specific physiology through the use of differentiation protocols. Still, existing LCL banks represent an important source of starting material for iPSC generation, and it is possible that the disruptions in gene regulation associated with long-term LCL maintenance could persist through the reprogramming process. To address this concern, we studied the effect of reprogramming mature LCL cultures from six unrelated donors to iPSCs on the ensuing gene expression patterns within and between individuals. We show that the reprogramming process results in a recovery of donor-specific gene regulatory signatures, increasing the number of genes with a detectable donor effect by an order of magnitude. The proportion of variation in gene expression statistically attributed to donor increases from 6.9% in LCLs to 24.5% in iPSCs (P < 10-15). Since environmental contributions are unlikely to be a source of individual variation in our system of highly passaged cultured cell lines, our observations suggest that the effect of genotype on gene regulation is more pronounced in iPSCs than in LCLs. Our findings indicate that iPSCs can be a powerful model system for studies of phenotypic variation across individuals in general, and the genetic association with variation in gene regulation in particular. We further conclude that LCLs are an appropriate starting material for iPSC generation.
Collapse
Affiliation(s)
- Samantha M. Thomas
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Courtney Kagan
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Bryan J. Pavlovic
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan Burnett
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Kristen Patterson
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan K. Pritchard
- Departments of Genetics and Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
| | - Yoav Gilad
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| |
Collapse
|
4
|
Yuan Y, Tian L, Lu D, Xu S. Analysis of genome-wide RNA-sequencing data suggests age of the CEPH/Utah (CEU) lymphoblastoid cell lines systematically biases gene expression profiles. Sci Rep 2015; 5:7960. [PMID: 25609584 PMCID: PMC4302305 DOI: 10.1038/srep07960] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/29/2014] [Indexed: 01/19/2023] Open
Abstract
In human, Lymphoblastoid cell lines (LCLs) from the CEPH/CEU (Centre d'Etude du Polymorphisme Humain – Utah) family resource have been extensively used for examining the genetics of gene expression levels. However, we noted that CEU/CEPH cell lines were collected and transformed approximately thirty years ago, much earlier than the other cell lines from the pertaining individuals, which we suspected could potentially affect gene expression, data analysis and results interpretation. In this study, by analyzing RNA sequencing data of CEU and the other three European populations as well as an African population, we systematically examined and evaluated the potential confounding effect of LCL age on gene expression levels and patterns. Our results indicated that gene expression profiles of CEU samples have been biased by the older age of CEU cell lines. Interestingly, most of CEU-specific expressions are associated with functions related to cell proliferation, which are more likely due to older age of cell lines than intrinsic characters of the population. We suggested the results be carefully explained when CEU LCLs are used for transcriptomic data analysis in future studies.
Collapse
Affiliation(s)
- Yuan Yuan
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max-Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lei Tian
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max-Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dongsheng Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max-Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max-Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
5
|
Nickles D, Madireddy L, Yang S, Khankhanian P, Lincoln S, Hauser SL, Oksenberg JR, Baranzini SE. In depth comparison of an individual's DNA and its lymphoblastoid cell line using whole genome sequencing. BMC Genomics 2012; 13:477. [PMID: 22974163 PMCID: PMC3473256 DOI: 10.1186/1471-2164-13-477] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 09/05/2012] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A detailed analysis of whole genomes can be now achieved with next generation sequencing. Epstein Barr Virus (EBV) transformation is a widely used strategy in clinical research to obtain an unlimited source of a subject's DNA. Although the mechanism of transformation and immortalization by EBV is relatively well known at the transcriptional and proteomic level, the genetic consequences of EBV transformation are less well understood. A detailed analysis of the genetic alterations introduced by EBV transformation is highly relevant, as it will inform on the usefulness and limitations of this approach. RESULTS We used whole genome sequencing to assess the genomic signature of a low-passage lymphoblastoid cell line (LCL). Specifically, we sequenced the full genome (40X) of an individual using DNA purified from fresh whole blood as well as DNA from his LCL. A total of 217.33 Gb of sequence were generated from the cell line and 238.95 Gb from the normal genomic DNA. We determined with high confidence that 99.2% of the genomes were identical, with no reproducible changes in structural variation (chromosomal rearrangements and copy number variations) or insertion/deletion polymorphisms (indels). CONCLUSIONS Our results suggest that, at this level of resolution, the LCL is genetically indistinguishable from its genomic counterpart and therefore their use in clinical research is not likely to introduce a significant bias.
Collapse
Affiliation(s)
- Dorothee Nickles
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143-0435, USA
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Morcos L, Ge B, Koka V, Lam KCL, Pokholok DK, Gunderson KL, Montpetit A, Verlaan DJ, Pastinen T. Genome-wide assessment of imprinted expression in human cells. Genome Biol 2011; 12:R25. [PMID: 21418647 PMCID: PMC3129675 DOI: 10.1186/gb-2011-12-3-r25] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/21/2011] [Accepted: 03/21/2011] [Indexed: 01/19/2023] Open
Abstract
Background Parent-of-origin-dependent expression of alleles, imprinting, has been suggested to impact a substantial proportion of mammalian genes. Its discovery requires allele-specific detection of expressed transcripts, but in some cases detected allelic expression bias has been interpreted as imprinting without demonstrating compatible transmission patterns and excluding heritable variation. Therefore, we utilized a genome-wide tool exploiting high density genotyping arrays in parallel measurements of genotypes in RNA and DNA to determine allelic expression across the transcriptome in lymphoblastoid cell lines (LCLs) and skin fibroblasts derived from families. Results We were able to validate 43% of imprinted genes with previous demonstration of compatible transmission patterns in LCLs and fibroblasts. In contrast, we only validated 8% of genes suggested to be imprinted in the literature, but without clear evidence of parent-of-origin-determined expression. We also detected five novel imprinted genes and delineated regions of imprinted expression surrounding annotated imprinted genes. More subtle parent-of-origin-dependent expression, or partial imprinting, could be verified in four genes. Despite higher prevalence of monoallelic expression, immortalized LCLs showed consistent imprinting in fewer loci than primary cells. Random monoallelic expression has previously been observed in LCLs and we show that random monoallelic expression in LCLs can be partly explained by aberrant methylation in the genome. Conclusions Our results indicate that widespread parent-of-origin-dependent expression observed recently in rodents is unlikely to be captured by assessment of human cells derived from adult tissues where genome-wide assessment of both primary and immortalized cells yields few new imprinted loci.
Collapse
Affiliation(s)
- Lisanne Morcos
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, Quebec, H3A 1A4, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics 2011; 187:1225-34. [PMID: 21321133 DOI: 10.1534/genetics.110.126177] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Changes in gene regulation are thought to play an important role in speciation and adaptation, especially in primates. However, we still know relatively little about the mechanisms underlying regulatory evolution. In particular, the extent to which epigenetic modifications underlie gene expression differences between primates is not yet known. Our study focuses on an epigenetic histone modification, H3K4me3, which is thought to promote transcription. To investigate the contribution of H3K4me3 to regulatory differences between species, we collected gene expression data and identified H3K4me3-associated genomic regions in lymphoblastoid cell lines (LCLs) from humans, chimpanzees, and rhesus macaques, using three cell lines from each species. We found strong evidence for conservation of H3K4me3 localization in primates. Moreover, regardless of species, H3K4me3 is consistently enriched near annotated transcription start sites (TSS), and highly expressed genes are more likely than lowly expressed genes to have the histone modification near their TSS. Interestingly, we observed an enrichment of interspecies differences in H3K4me3 at the TSS of genes that are differentially expressed between species. We estimate that as much as 7% of gene expression differences between the LCLs of humans, chimpanzees, and rhesus macaques may be explained, at least in part, by changes in the status of H3K4me3 histone modifications. Our results suggest a modest, yet important role for epigenetic changes in gene expression differences between primates.
Collapse
|
8
|
Caliskan M, Cusanovich DA, Ober C, Gilad Y. The effects of EBV transformation on gene expression levels and methylation profiles. Hum Mol Genet 2011; 20:1643-52. [PMID: 21289059 DOI: 10.1093/hmg/ddr041] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Epstein-Barr virus (EBV) transformed lymphoblastoid cell lines (LCLs) provide a conveniently accessible and renewable resource for functional genomic studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. A lingering concern, however, is that the changes associated with EBV transformation of B cells reduce the usefulness of LCLs as a surrogate model for primary tissues. To evaluate the validity of this concern, we compared global gene expression and methylation profiles between CD20+ primary B cells sampled from six individuals and six independent replicates of transformed LCLs derived from each sample. These data allowed us to obtain a detailed catalog of the genes and pathways whose regulation is affected by EBV transformation. We found that the expression levels and promoter methylation profiles of more than half of the studied genes were affected by the EBV transformation, including enrichments of genes involved in transcription regulation, cell cycle and immune response. However, we show that most of the differences in gene expression levels between LCLs and B cells are of small magnitude, and that LCLs can often recapitulate the naturally occurring gene expression variation in primary B cells. Thus, our observations suggest that inference of the genetic architecture that underlies regulatory variation in LCLs can typically be generalized to primary B cells. In contrast, inference based on functional studies in LCLs may be more limited to the cell lines.
Collapse
Affiliation(s)
- Minal Caliskan
- Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
| | | | | | | |
Collapse
|
9
|
Norris-Kirby A, Hagenkord JM, Kshirsagar MP, Ronnett BM, Murphy KM. Abnormal villous morphology associated with triple trisomy of paternal origin. J Mol Diagn 2010; 12:525-9. [PMID: 20413680 DOI: 10.2353/jmoldx.2010.090184] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The vast majority of trisomies in spontaneous abortions (SAB) are single and of maternal origin, most frequently due to meiosis I errors. Triple trisomies are exceedingly rare (approximately 0.05% of spontaneous abortions), most often of maternal origin, and associated with increased maternal age. Some trisomic SAB specimens can exhibit abnormal villous morphology simulating a partial hydatidiform mole, a distinct form of hydatidiform mole characterized by diandric triploidy. A SAB specimen from a 27-year-old woman, G1P0 at 8 weeks gestational age, was reviewed in consultation to address the finding of morphological features suggestive of a partial hydatidiform mole but DNA ploidy analysis yielding a diploid result. The villi were irregularly shaped and hydropic but lacked trophoblastic hyperplasia; p57 expression was retained. Since fully developed features of a partial hydatidiform mole were lacking, additional analysis was performed. Molecular genotyping and single nucleotide polymorphism array analysis demonstrated biparental diploidy with trisomy of chromosomes 7, 13, and 20, all of paternal origin. The three trisomies may have originated from paternal meiosis II errors, or from mitotic nondisjunction. We believe this to be the first report of triple trisomy in a SAB confirmed to be of paternal origin.
Collapse
Affiliation(s)
- Alexis Norris-Kirby
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | | | | | | | | |
Collapse
|
10
|
Abstract
Variation in gene expression constitutes an important source of biological variability within and between populations that is likely to contribute significantly to phenotypic diversity. Recent conceptual, technical, and methodological advances have enabled the genome-scale dissection of transcriptional variation. Here, we outline common approaches for detecting gene expression quantitative trait loci, and summarize the insights gleaned from these studies regarding the genetic architecture of transcriptional variation and the nature of regulatory alleles. Particular emphasis is placed on human studies, and we discuss experimental designs that ensure that increasingly large and complex studies continue to advance our understanding of gene expression variation. We conclude by discussing the evolution of gene expression levels, and we explore prospects for leveraging new technological developments to investigate inherited variation in gene expression in even greater depth.
Collapse
Affiliation(s)
- Daniel A Skelly
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA.
| | | | | |
Collapse
|
11
|
Bullaughey K, Chavarria CI, Coop G, Gilad Y. Expression quantitative trait loci detected in cell lines are often present in primary tissues. Hum Mol Genet 2009; 18:4296-303. [PMID: 19671653 DOI: 10.1093/hmg/ddp382] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Expression quantitative trait loci (eQTL) mapping is a powerful tool for identifying genetic regulatory variation. However, at present, most eQTLs in humans were identified using gene expression data from cell lines, and it remains unknown whether these eQTLs also have a regulatory function in other expression contexts, such as human primary tissues. Here we investigate this question using a targeted strategy. Specifically, we selected a subset of large-effect eQTLs identified in the HapMap lymphoblastoid cell lines, and examined the association of these eQTLs with gene expression levels across individuals in five human primary tissues (heart, kidney, liver, lung and testes). We show that genotypes at the eQTLs we selected are often predictive of variation in gene expression levels in one or more of the five primary tissues. The genotype effects in the primary tissues are consistently in the same direction as the effects inferred in the cell lines. Additionally, a number of the eQTLs we tested are found in more than one of the tissues. Our results indicate that functional studies in cell lines may uncover a substantial amount of genetic variation that affects gene expression levels in human primary tissues.
Collapse
Affiliation(s)
- Kevin Bullaughey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | | | | | | |
Collapse
|
12
|
Mencarelli MA, Katzaki E, Papa FT, Sampieri K, Caselli R, Uliana V, Pollazzon M, Canitano R, Mostardini R, Grosso S, Longo I, Ariani F, Meloni I, Hayek J, Balestri P, Mari F, Renieri A. Private inherited microdeletion/microduplications: Implications in clinical practice. Eur J Med Genet 2008; 51:409-16. [DOI: 10.1016/j.ejmg.2008.06.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Accepted: 06/17/2008] [Indexed: 11/29/2022]
|
13
|
Schüle B, Li HH, Fisch-Kohl C, Purmann C, Francke U. DLX5 and DLX6 expression is biallelic and not modulated by MeCP2 deficiency. Am J Hum Genet 2007; 81:492-506. [PMID: 17701895 PMCID: PMC1950824 DOI: 10.1086/520063] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Accepted: 05/21/2007] [Indexed: 11/03/2022] Open
Abstract
Mutations in MECP2 and Mecp2 (encoding methyl-CpG binding protein 2 [MeCP2]) cause distinct neurological phenotypes in humans and mice, respectively, but the molecular pathology is unclear. Recent literature claimed that the developmental homeobox gene DLX5 is imprinted and that its imprinting status is modulated by MeCP2, leading to biallelic expression in Rett syndrome and twofold overexpression of Dlx5 and Dlx6 in Mecp2-null mice. The conclusion that DLX5 is a direct target of MeCP2 has implications for research on the molecular bases of Rett syndrome, autism, and genomic imprinting. Attempting to replicate the reported data, we evaluated allele-specific expression of DLX5 and DLX6 in mouse x human somatic cell hybrids, lymphoblastoid cell lines, and frontal cortex from controls and individuals with MECP2 mutations. We identified novel single-nucleotide polymorphisms in DLX5 and DLX6, enabling the first imprinting studies of DLX6. We found that DLX5 and DLX6 are biallelically expressed in somatic cell hybrids and in human cell lines and brain, with no differences between affected and control samples. We also determined expression levels of Dlx5 and Dlx6 in forebrain from seven male Mecp2-mutant mice and eight wild-type littermates by real-time quantitative reverse-transcriptase polymerase chain reaction assays. Expression of Dlx5 and Dlx6, as well as of the imprinted gene Peg3, in mouse forebrain was highly variable, with no consistent differences between Mecp2-null mutants and controls. We conclude that DLX5 and DLX6 are not imprinted in humans and are not likely to be direct targets of MeCP2 modulation. In contrast, the imprinting status of PEG3 and PEG10 is maintained in MeCP2-deficient tissues. Our results confirm that MeCP2 plays no role in the maintenance of genomic imprinting and add PEG3 and PEG10 to the list of studied imprinted genes.
Collapse
Affiliation(s)
- Birgitt Schüle
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | | |
Collapse
|
14
|
Philibert R, Madan A, Andersen A, Cadoret R, Packer H, Sandhu H. Serotonin transporter mRNA levels are associated with the methylation of an upstream CpG island. Am J Med Genet B Neuropsychiatr Genet 2007; 144B:101-5. [PMID: 16958039 DOI: 10.1002/ajmg.b.30414] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The serotonin reuptake transporter (5HTT) is thought to be the principal regulator of serotonergic activity and epigenetic effects at this locus are thought to be important moderators of vulnerability to neuropsychiatric illness. In attempt to understand the basis of this regulation, several gene polymorphisms that affect 5HTT mRNA levels have been described. But to date, no clear mechanism linking these polymorphisms to vulnerability to epigenetic effects have been described. In this communication, we describe a CpG island in the 5' region of the 5HTT gene that contains an alternative exon 1 and possible promoter for 5HTT. We then confirm the existence of this transcript and ascertain the methylation status of this CpG island in 49 lymphoblast cell lines and analyze the relationship between methylation and 5HTT mRNA levels. We demonstrate that methylation at this CpG island is associated with decreased levels of 5HTT mRNA, but that this effect is evident only when 5HTTLPR genotype is taken into account. We suggest that these findings have significant implications for the understanding of the role of this locus in behavioral illness.
Collapse
Affiliation(s)
- Robert Philibert
- Department of Psychiatry, The University of Iowa, Psychiatry Research/MEB, Iowa City, Iowa, USA.
| | | | | | | | | | | |
Collapse
|
15
|
Abstract
The promise of human embryonic stem cell (hESC) lines for treating injuries and degenerative diseases, for understanding early human development, for disease modelling and for drug discovery, has brought much excitement to scientific communities as well as to the public. Although all of the lines derived worldwide share the expression of characteristic pluripotency markers, many differences are emerging between lines that may be more associated with the wide range of culture conditions in current use than the inherent genetic variation of the embryos from which embryonic stem cells were derived. Thus, the validity of many comparisons between lines published thus far is difficult to interpret. This article reviews the evidence for differences between lines, focusing on studies of pluripotency marker molecules, transcriptional profiling, genetic stability and epigenetic stability, for which there is most evidence. Recognition and assessment of environmentally induced differences will be important to facilitate the development of culture systems that maximize stability in culture and provide lines with maximal potential for safety and success in the range of possible applications.
Collapse
Affiliation(s)
- C Allegrucci
- School of Human Development, University of Nottingham, Queens Medical Centre, Nottingham, UK
| | | |
Collapse
|
16
|
Pastinen T, Ge B, Hudson TJ. Influence of human genome polymorphism on gene expression. Hum Mol Genet 2006; 15 Spec No 1:R9-16. [PMID: 16651375 DOI: 10.1093/hmg/ddl044] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genetic variation, through its effects on gene expression, plays a crucial role in phenotypic variation and disease susceptibility. Recent studies from our group and others have integrated a number of resources and technologies to assess several aspects of genome variation affecting gene expression. Some of these large-scale mapping studies involving expression quantitative traits have recently been reviewed [Gibson, G. and Weir, B. (2005) The quantitative genetics of transcription. Trends Genet., 21, 616-623; de Koning, D.J. and Haley, C.S. (2005) Genetical genomics in humans and model organisms. Trends Genet., 21, 377-381], with particular attention to the statistical issues. In this review, we compare allele-specific expression studies in human samples (primarily lymphoblastoid cell lines from the CEPH HapMap panel), as a prelude to a discussion on study design issues and sources of variation, in order to propose the steps required to build a detailed map of cis-acting regulatory variation in the human genome. Obtaining panels of tissues from large numbers of individuals remains an important limitation. We also conclude that there is insufficient knowledge as to the feasibility of comprehensive studies of trans-acting variation in the human genome.
Collapse
Affiliation(s)
- Tomi Pastinen
- Genome Quebec Innovation Centre, McGill University, Room 7105, 740 Dr Penfield Avenue, Montreal, Que., Canada H3A 1A4
| | | | | |
Collapse
|
17
|
Bán Z, Nagy B, Papp C, Beke A, Tóth-Pál E, Papp Z. Recurrent Trisomy 21 and Uniparental Disomy 21 in a Family. Fetal Diagn Ther 2003; 18:454-8. [PMID: 14564119 DOI: 10.1159/000073142] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Accepted: 12/20/2002] [Indexed: 11/19/2022]
Abstract
OBJECTIVE A 32-year-old pregnant woman was referred to our genetic counselling because of recurrent trisomy 21 in the family. Analysis of amniotic fluid cell culture revealed karyotype 47,XY+21 of the fetus. METHODS Karyotyping and molecular analysis were undertaken in the fetal and parental samples to determine the origin of the extra chromosome 21. RESULTS Both parents had a normal blood karyotype. Microsatellite marker analysis showed maternal origin of the fetal extra chromosome 21. As the mother showed homozygosity for all investigated markers on chromosome 21, we also tested her family. We detected the same homozygosity in some family members which was consistent with isodisomy of the chromosome 21 caused by uniparental disomy (UPD). CONCLUSIONS Here we report on a family in which multiple aneuploid conceptions occurred with trisomy 21, and molecular analysis showed that the euploidy of the investigated healthy family members is due to UPD21. This observation stresses the importance of prenatal cytogenetic and molecular analysis in case of parental UPD.
Collapse
Affiliation(s)
- Zoltán Bán
- 1st Department of Obstetrics and Gynaecology, Semmelweis University, Budapest, Hungary.
| | | | | | | | | | | |
Collapse
|
18
|
O’Brien EK, Zhang X, Nishimura C, Tomblin JB, Murray JC. Association of specific language impairment (SLI) to the region of 7q31. Am J Hum Genet 2003; 72:1536-43. [PMID: 12721956 PMCID: PMC1180313 DOI: 10.1086/375403] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2002] [Accepted: 03/04/2003] [Indexed: 11/03/2022] Open
Abstract
FOXP2 (forkhead box P2) was the first gene characterized in which a mutation affects human speech and language abilities. A common developmental language disorder, specific language impairment (SLI), affects 6%-7% of children with normal nonverbal intelligence and has evidence of a genetic basis in familial and twin studies. FOXP2 is located on chromosome 7q31, and studies of other disorders with speech and language impairment, including autism, have found linkage to this region. In the present study, samples from children with SLI and their family members were used to study linkage and association of SLI to markers within and around FOXP2, and samples from 96 probands with SLI were directly sequenced for the mutation in exon 14 of FOXP2. No mutations were found in exon 14 of FOXP2, but strong association was found to a marker within the CFTR gene and another marker on 7q31, D7S3052, both adjacent to FOXP2, suggesting that genetic factors for regulation of common language impairment reside in the vicinity of FOXP2.
Collapse
Affiliation(s)
- Erin K. O’Brien
- Departments of Otolaryngology, Speech Pathology and Audiology, and Pediatrics, University of Iowa, Iowa City
| | - Xuyang Zhang
- Departments of Otolaryngology, Speech Pathology and Audiology, and Pediatrics, University of Iowa, Iowa City
| | - Carla Nishimura
- Departments of Otolaryngology, Speech Pathology and Audiology, and Pediatrics, University of Iowa, Iowa City
| | - J. Bruce Tomblin
- Departments of Otolaryngology, Speech Pathology and Audiology, and Pediatrics, University of Iowa, Iowa City
| | - Jeffrey C. Murray
- Departments of Otolaryngology, Speech Pathology and Audiology, and Pediatrics, University of Iowa, Iowa City
| |
Collapse
|
19
|
Rickard SJ, Wilson LC. Analysis of GNAS1 and overlapping transcripts identifies the parental origin of mutations in patients with sporadic Albright hereditary osteodystrophy and reveals a model system in which to observe the effects of splicing mutations on translated and untranslated messenger RNA. Am J Hum Genet 2003; 72:961-74. [PMID: 12624854 PMCID: PMC1180358 DOI: 10.1086/374566] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2002] [Accepted: 01/16/2003] [Indexed: 11/03/2022] Open
Abstract
Albright hereditary osteodystrophy (AHO) is caused by heterozygous deactivating GNAS1 mutations. There is a parent-of-origin effect. Maternally derived mutations are usually associated with resistance to parathyroid hormone termed "pseudohypoparathyroidism type Ia." Paternally derived mutations are associated with AHO but usually normal hormone responsiveness, known as "pseudo-pseudohypoparathyroidism." These observations can be explained by tissue-specific GNAS1 imprinting. Regulation of the genomic region that encompasses GNAS1 is complex. At least three upstream exons that splice to exon 2 of GNAS1 and that are imprinted have been reported. NESP55 is exclusively maternally expressed, whereas exon 1A and XL alphas are exclusively paternally expressed. We set out to identify the parental origin of GNAS1 mutations in patients with AHO by searching for their mutation in the overlapping transcripts. This information would be of value in patients with sporadic disease, for predicting their endocrine phenotype and planning follow-up. In doing so, we identified mutations that resulted in nonsense-mediated decay of the mutant Gs alpha transcript but that were detectable in NESP55 messenger RNA (mRNA), probably because they lie within its 3' untranslated region. Analysis of the NESP55 transcripts revealed the creation of a novel splice site in one patient and an unusual intronic mutation that caused retention of the intron in a further patient, neither of which could be detected by analysis of the Gs alpha complementary DNA. This cluster of overlapping transcripts represents a useful model system in which to analyze the effects that mutant sequence has on mRNA-in particular, splicing-and the mechanisms of nonsense-mediated mRNA decay.
Collapse
Affiliation(s)
- Sarah J Rickard
- Clinical and Molecular Genetics Unit, Institute of Child Health, and Great Ormond Street Hospital NHS Trust, London, United Kingdom
| | | |
Collapse
|
20
|
Okamoto K, Horisawa R, Kawamura T, Asai A, Ogino M, Takagi T, Ohno Y. Family history and risk of subarachnoid hemorrhage: a case-control study in Nagoya, Japan. Stroke 2003; 34:422-6. [PMID: 12574554 DOI: 10.1161/01.str.0000053851.17964.c6] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND PURPOSE We sought to examine the relation between a family history of subarachnoid hemorrhage (SAH) and the risk of SAH by using a case-control study. METHODS Case subjects consisted of a consecutive series of 195 patients with spontaneous SAH, aged 30 to 79 years, with aneurysms confirmed by angiography and/or CT scan. Hospital and community control subjects were identified and matched to each case by sex and age (+/-2 years). Multiple conditional logistic regression was used to calculate the odds ratio (OR) and 95% interval (CI) adjusted for potential confounders. RESULTS Having a family member with SAH was significantly associated with an increased risk of SAH (OR, 4.0, 95% CI, 2.0 to 8.0), after adjusting for potential confounders. The risk for a positive family history of SAH was similar for men and women and was inversely related to the SAH patient's age. A maternal positive SAH history (OR, 5.4; 95% CI, 1.8 to 16.0) posed a much greater risk than a paternal positive history (OR, 3.2, 95% CI, 1.1 to 13.4). CONCLUSIONS A positive family history of SAH was significantly and strongly associated with the risk of SAH. To prevent the onset of SAH at a younger age, much more attention should be given to individuals with any family member (first-degree relatives) suffering SAH episodes.
Collapse
Affiliation(s)
- Kazushi Okamoto
- Department of Public Health, Aichi Prefectural College of Nursing and Health, Nagoya, Japan.
| | | | | | | | | | | | | |
Collapse
|
21
|
Tentler D, Brandberg G, Betancur C, Gillberg C, Annerén G, Orsmark C, Green ED, Carlsson B, Dahl N. A balanced reciprocal translocation t(5;7)(q14;q32) associated with autistic disorder: molecular analysis of the chromosome 7 breakpoint. AMERICAN JOURNAL OF MEDICAL GENETICS 2001; 105:729-36. [PMID: 11803521 DOI: 10.1002/ajmg.1607] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Autism is a neuropsychiatric disorder characterized by impairments in social interaction, restricted and stereotypic pattern of interest with onset by 3 years of age. The results of genetic linkage studied for autistic disorder (AD) have suggested a susceptibility locus for the disease on the long arm of chromosome 7. We report a girl with AD and a balanced reciprocal translocation t(5;7)(q14;q32). The mother carries the translocation but do not express the disease. Fluorescent in situ hybridization (FISH) analysis with chromosome 7-specific YAC clones showed that the breakpoint coincides with the candidate region for AD. We identified a PAC clone that spans the translocation breakpoint and the breakpoint was mapped to a 2 kb region. Mutation screening of the genes SSBP and T2R3 located just centromeric to the breakpoint was performed in a set of 29 unrelated autistic sibling pairs who shared at least one chromosome 7 haplotype. We found no sequence variations, which predict amino acid alterations. Two single nucleotide polymorphisms were identified in the T2R3 gene, and associations between allele variants and AD in our population were not found. The methylation pattern of different chromosome 7 regions in the patient's genomic DNA appears normal. Here we report the clinical presentation of the patient with AD and the characterization of the genomic organization across the breakpoint at 7q32. The precise localization of the breakpoint on 7q32 may be relevant for further linkage studies and molecular analysis of AD in this region.
Collapse
Affiliation(s)
- D Tentler
- Department of Genetics and Pathology, Section of Clinical Genetics, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
| | | | | | | | | | | | | | | | | |
Collapse
|