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1.  Candidate genes for Alzheimer’s disease are associated with individual differences in plasma levels of beta amyloid peptides in adults with Down syndrome 
Neurobiology of aging  2015;36(10):2907.e1-2907.e10.
We examined the contribution of candidate genes for Alzheimer’s disease (AD) on Chromosome 21 and other chromosomes to differences in Aβ peptide levels in a cohort of adults with DS, a population at high risk for AD. Participants were 254 non-demented adults with Down syndrome, 30–78 years of age. Genomic DNA was genotyped using an Illumina GoldenGate custom array. We used linear regression to examine differences in levels of Aβ peptides associated with the number of risk alleles, adjusting for age, sex, level of intellectual disability, race/ethnicity and the presence of the APOE ε4 allele. For Aβ42 levels, the strongest gene-wise association was found for a SNP on CAHLM1; for Aβ40 levels the strongest gene-wise associations were found for SNPs in IDE and SOD1, while the strongest gene-wise associations with levels of the Aβ42/Aβ40 ratio were found for SNPs in SORCS1. Broadly classified, variants in these genes may influence APP processing (CALHM1, IDE), vesicular trafficking (SORCS1), and response to oxidative stress (SOD1).
PMCID: PMC4562880  PMID: 26166206
Down syndrome; β amyloid peptides; genetics; biomarkers
2.  Distress During Pregnancy: Epigenetic Regulation of Placenta Glucocorticoid-Related Genes and Fetal Neurobehavior 
The American journal of psychiatry  2016;173(7):705-713.
Increased risk of psychopathology is observed in children exposed to maternal prenatal distress, and elevated maternal cortisol and epigenetic regulation of placental glucocorticoid-pathway genes are potential mechanisms. The authors examined maternal distress and salivary cortisol in relation to fetal movement and heart rate (“coupling”) and DNA methylation of three glucocorticoid pathway genes—HSD11B2, NR3C1, and FKBP5—in term placentas.
Mood questionnaires and salivary cortisol were collected from 61 women between 24–27 gestational weeks, and fetal assessment was conducted at 34–37 weeks. Placental CpG methylation in the three genes was analyzed using 450K Beadchips and bisulfite sequencing; correlations between maternal and fetal variables and DNA methylation were tested; and maternal distress effects on fetal behavior via DNA methylation were investigated.
Perceived stress (Perceived Stress Scale), but not cortisol, was associated with altered CpG methylation in placentas. In the highest tertile of the Perceived Stress Scale, the Beadchip data revealed modestly elevated methylation of HSD11B2, associated with lower fetal coupling (β=−0.51), and modestly elevated methylation of FKBP5, also with lower fetal coupling (β=−0.47). These increases in methylation were validated by bisulfite sequencing, where they occurred in a minority of clones.
This is the first study to link the effects of pregnant women’s distress on the fetus and epigenetic changes in placental genes. Since increased DNA methylation in HSD11B2 and FKBP5 are seen in a minority of bisulfite sequencing clones, these epigenetic changes, and functional consequences, may affect subpopulations of placental cells.
PMCID: PMC5026410  PMID: 27013342
4.  Down syndrome and Alzheimer's disease: Common pathways, common goals 
In the United States, estimates indicate there are between 250,000 and 400,000 individuals with Down syndrome (DS), and nearly all will develop Alzheimer's disease (AD) pathology starting in their 30s. With the current lifespan being 55 to 60 years, approximately 70% will develop dementia, and if their life expectancy continues to increase, the number of individuals developing AD will concomitantly increase. Pathogenic and mechanistic links between DS and Alzheimer's prompted the Alzheimer's Association to partner with the Linda Crnic Institute for Down Syndrome and the Global Down Syndrome Foundation at a workshop of AD and DS experts to discuss similarities and differences, challenges, and future directions for this field. The workshop articulated a set of research priorities: (1) target identification and drug development, (2) clinical and pathological staging, (3) cognitive assessment and clinical trials, and (4) partnerships and collaborations with the ultimate goal to deliver effective disease-modifying treatments.
PMCID: PMC4817997  PMID: 25510383
Down syndrome; Alzheimer's disease; Dementia; Animal models; Ts65Dn; Drug discovery; Neuroinflammation; Cognitive assessment; Amyloid precursor protein; Beta-amyloid; Tau; Clinical trials; Biomarkers; Trisomy 21; ADNI; DS-Connect; Neuroimaging; Workshop
5.  Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models 
Genome Biology  2015;16:263.
Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood.
Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in each of these cell types. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites (TFBSs), implicating a mechanism involving altered TFBS occupancy. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects.
These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-015-0827-6) contains supplementary material, which is available to authorized users.
PMCID: PMC4659173  PMID: 26607552
6.  Integrative epigenomic and genomic filtering for methylation markers in hepatocellular carcinomas 
BMC Medical Genomics  2015;8:28.
Epigenome-wide studies in hepatocellular carcinoma (HCC) have identified numerous genes with aberrant DNA methylation. However, methods for triaging functional candidate genes as useful biomarkers for epidemiological study have not yet been developed.
We conducted targeted next-generation bisulfite sequencing (bis-seq) to investigate associations of DNA methylation and mRNA expression in HCC. Integrative analyses of epigenetic profiles with DNA copy number analysis were used to pinpoint functional genes regulated mainly by altered DNA methylation.
Significant differences between HCC tumor and adjacent non-tumor tissue were observed for 28 bis-seq amplicons, with methylation differences varying from 12% to 43%. Available mRNA expression data in Oncomine were evaluated. Two candidate genes (GRASP and TSPYL5) were significantly under-expressed in HCC tumors in comparison with precursor and normal liver tissues. The expression levels in tumor tissues were, respectively, 1.828 and − 0.148, significantly lower than those in both precursor and normal liver tissue. Validations in an additional 42 paired tissues showed consistent under-expression in tumor tissue for GRASP (−7.49) and TSPYL5 (−9.71). A highly consistent DNA hypermethylation and mRNA repression pattern was obtained for both GRASP (69%) and TSPYL5 (73%), suggesting that their biological function is regulated by DNA methylation. Another two genes (RGS17 and NR2E1) at Chr6q showed significantly decreased DNA methylation in tumors with loss of DNA copy number compared to those without, suggesting alternative roles of DNA copy number losses and hypermethylation in the regulation of RGS17 and NR2E1.
These results suggest that integrative analyses of epigenomic and genomic data provide an efficient way to filter functional biomarkers for future epidemiological studies in human cancers.
Electronic supplementary material
The online version of this article (doi:10.1186/s12920-015-0105-1) contains supplementary material, which is available to authorized users.
PMCID: PMC4460673  PMID: 26059414
7.  Genetic Epidemiology and Nonsyndromic Structural Birth Defects: From Candidate Genes to Epigenetics 
JAMA pediatrics  2014;168(4):371-377.
Birth defects are a leading cause of infant morbidity and mortality worldwide. The vast majority of birth defects are nonsyndromic, and although their etiologies remain mostly unknown, evidence supports the hypothesis that they result from the complex interaction of genetic, epigenetic, environmental, and lifestyle factors. Since our last review published in 2002 describing the basic tools of genetic epidemiology used to study nonsyndromic structural birth defects, many new approaches have become available and have been used with varying success. Through rapid advances in genomic technologies, investigators are now able to interrogate large portions of the genome at a fraction of previous costs. With next generation sequencing (NGS), research has progressed from assessing a small percentage of single nucleotide polymorphisms (SNPs) to assessing the entire human protein-coding repertoire (exome) – an approach that is starting to uncover rare but informative mutations associated with nonsyndromic birth defects. Here we report on the current state of genetic epidemiology of birth defects and comment on future challenges and opportunities. We consider issues of study design, and we discuss common variant approaches including candidate gene studies and genome-wide association studies (GWAS). We also discuss the complexities embedded in exploring gene-environment interactions. We complete our review by describing new and promising NGS technologies and examining how the study of epigenetic mechanisms could become the key to unraveling the complex etiologies of nonsyndromic structural birth defects.
PMCID: PMC3981910  PMID: 24515445
8.  Intramuscular Therapeutic Vaccination Targeting HPV16 Induces T Cell Responses That Localize in Mucosal Lesions 
Science translational medicine  2014;6(221):221ra13.
About 25% of high-grade cervical intraepithelial neoplasias (CIN2/3) caused by human papillomavirus serotype 16 (HPV16) undergo complete spontaneous regression. However, to date, therapeutic vaccination strategies for HPV disease have yielded limited success when measured by their ability to induce robust peripheral blood T cell responses to vaccine antigen. We report marked immunologic changes in the target lesion microenvironment after intramuscular therapeutic vaccination targeting HPV16 E6/E7 antigens, in subjects with CIN2/3 who had modest detectable responses in circulating T lymphocytes. Histologic and molecular changes, including markedly (average threefold) increased intensity of CD8+ T cell infiltrates in both the stromal and epithelial compartments, suggest an effector response to vaccination. Postvaccination cervical tissue immune infiltrates included organized tertiary lymphoid-like structures in the stroma subjacent to residual intraepithelial lesions and, unlike infiltrates in unvaccinated lesions, showed evidence of proliferation induced by recognition of cognate antigen. At a molecular level, these histologic changes in the stroma were characterized by increased expression of genes associated with immune activation (CXCR3) and effector function (Tbet and IFNβ), and were also associated with an immunologic signature in the overlying dysplastic epithelium. High-throughput T cell receptor sequencing of unmanipulated specimens identified clonal expansions in the tissue that were not readily detectable in peripheral blood. Together, these findings indicate that peripheral therapeutic vaccination to HPV antigens can induce a robust tissue-localized effector immune response, and that analyses of immune responses at sites of antigen are likely to be much more informative than analyses of cells that remain in the circulation.
PMCID: PMC4086631  PMID: 24477000
9.  Creation and characterization of BAC-transgenic mice with physiological over-expression of epitope-tagged RCAN1 (DSCR1) 
The chromosome 21 gene RCAN1, encoding a modulator of the calcineurin (CaN) phosphatase, is a candidate gene for contributing to cognitive disability in people with Down syndrome (DS; trisomy 21). To develop a physiologically relevant model for studying the biochemistry of RCAN1 and its contribution to DS, we generated bacterial artificial chromosome-transgenic (BAC-Tg) mouse lines containing the human RCAN1 gene with a C-terminal HA-FLAG epitope tag incorporated by recombineering. The BAC-Tg was expressed at levels only moderately higher than the native Rcan1 gene; approximately 1.5-fold in RCAN1BAC-Tg1 and 2-fold in RCAN1BAC-Tg2. Affinity purification of the RCAN1 protein complex from brains of these mice revealed a core complex of RCAN1 with calcineurin (CaN), glycogen synthase kinase 3-beta (Gsk3b), and calmodulin, with sub-stoichiometric components including LOC73419. The BAC-Tg mice are fully viable, but long-term synaptic potentiation (LTP) is impaired in proportion to BAC-Tg dosage in hippocampal brain slices from these mice. RCAN1 can act as a tumor suppressor in some systems, but we found that the RCAN1 BAC-Tg did not reduce mammary cancer growth when present at a low copy number in Tp53;WAP-Cre mice. This work establishes a useful mouse model for investigating the biochemistry and dose-dependent functions of the RCAN1 protein in vivo.
PMCID: PMC3562396  PMID: 23096997
10.  Hypomethylating therapy in an aggressive stroma-rich model of pancreatic carcinoma 
Cancer research  2012;73(2):885-896.
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy that resists current treatments. To test epigenetic therapy against this cancer, we used the DNA demethylating drug 5-aza-2′-deoxycytidine (DAC) in an aggressive mouse model of stromal rich PDAC (KPC-Brca1 mice). In untreated tumors, we found globally decreased 5-methyl-cytosine (5mC) in malignant epithelial cells and in cancer-associated myofibroblasts (CAFs), along with increased amounts of 5-hydroxymethyl-cytosine (5HmC) in CAFs, in progression from pancreatic intraepithelial neoplasia (PanIN) to PDAC. DAC further reduced DNA methylation and slowed PDAC progression, markedly extending survival in an early treatment protocol and significantly though transiently inhibiting tumor growth when initiated later, without adverse side effects. Escaping tumors contained areas of sarcomatoid transformation with disappearance of CAFs. Mixing-allografting experiments and proliferation indices showed that DAC efficacy was due to inhibition of both the malignant epithelial cells and the CAFs. Expression profiling and immunohistochemistry highlighted DAC-induction of STAT1 in the tumors, and DAC plus gamma-interferon produced an additive anti-proliferative effect on PDAC cells. DAC induced strong expression of the testis antigen DAZL in CAFs. These data show that DAC is effective against PDAC in vivo and provide a rationale for future studies combining hypomethylating agents with cytokines and immunotherapy.
PMCID: PMC3548986  PMID: 23204224
11.  Stromal Protein Ecm1 Regulates Ureteric Bud Patterning and Branching 
PLoS ONE  2013;8(12):e84155.
The interactions between the nephrogenic mesenchyme and the ureteric bud during kidney development are well documented. While recent studies have shed some light on the importance of the stroma during renal development, many of the signals generated in the stroma, the genetic pathways and interaction networks involving the stroma are yet to be identified. Our previous studies demonstrate that retinoids are crucial for branching of the ureteric bud and for patterning of the cortical stroma. In the present study we demonstrate that autocrine retinoic acid (RA) signaling in stromal cells is critical for their survival and patterning, and show that Extracellular matrix 1, Ecm1, a gene that in humans causes irritable bowel syndrome and lipoid proteinosis, is a novel RA-regulated target in the developing kidney, which is secreted from the cortical stromal cells surrounding the cap mesenchyme and ureteric bud. Our studies suggest that Ecm1 is required in the ureteric bud for regulating the distribution of Ret which is normally restricted to the tips, as inhibition of Ecm1 results in an expanded domain of Ret expression and reduced numbers of branches. We propose a model in which retinoid signaling in the stroma activates expression of Ecm1, which in turn down-regulates Ret expression in the ureteric bud cleft, where bifurcation normally occurs and normal branching progresses.
PMCID: PMC3877229  PMID: 24391906
12.  Comparative Anatomy of Chromosomal Domains with Imprinted and Non-Imprinted Allele-Specific DNA Methylation 
PLoS Genetics  2013;9(8):e1003622.
Allele-specific DNA methylation (ASM) is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons), one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated) while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM. Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb. The ASM in the C3orf27-RPN1 intergenic region was placenta-specific and associated with allele-specific expression of a long non-coding RNA. Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR. Methylation mapping in two additional genes with non-imprinted haplotype-dependent ASM, ELK3 and CYP2A7, showed that the CYP2A7 DMR also overlaps a CTCF site. Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM. Arguing for biological importance, our analysis of published whole genome bis-seq data from hES cells revealed multiple genome-wide association study (GWAS) peaks near CTCF binding sites with ASM.
Author Summary
Allele-specific DNA methylation (ASM) is a central mechanism of gene regulation in humans, which can influence inter-individual differences in physical and mental traits and disease susceptibility. ASM is mediated either by parental imprinting, in which the repressed copy (allele) of the gene is determined by which type of parent (mother or father) transmitted it or, for a larger number of genes, by the local DNA sequence, independent of which parent transmitted it. Chromosomal regions with imprinted ASM have been well studied, and certain mechanistic principles, including the role of discrete differentially methylated regions (DMRs) and involvement of the insulator protein CTCF, have emerged. However, the molecular mechanisms underlying non-imprinted sequence-dependent ASM are not yet understood. Here we describe our detailed mapping of ASM across 5 gene regions, including two novel examples of imprinted ASM and three gene regions with non-imprinted, sequence-dependent ASM. Our data uncover shared molecular features – small discrete DMRs, and the binding of CTCF to these DMRs, in examples of both types of ASM. Combining ASM mapping with genetic association data suggests that sequence-dependent ASM at CTCF binding sites influences diverse human traits.
PMCID: PMC3757050  PMID: 24009515
13.  Estrogen Receptor-Beta Variants Are Associated with Increased Risk of Alzheimer's Disease in Women with Down Syndrome 
Genetic variants that affect estrogen activity may influence the risk of Alzheimer's disease (AD). We examined the relation of polymorphisms in the gene for the estrogen receptor-beta (ESR2) to the risk of AD in women with Down syndrome.
Two hundred and forty-nine women with Down syndrome, 31–70 years of age and nondemented at baseline, were followed at 14- to 18-month intervals for 4 years. Women were genotyped for 13 single-nucleotide polymorphisms (SNPs) in the ESR2 gene, and their association with AD incidence was examined.
Among postmenopausal women, we found a 2-fold increase in the risk of AD for women carrying 1 or 2 copies of the minor allele at 3 SNPs in introns seven (rs17766755) and six (rs4365213 and rs12435857) and 1 SNP in intron eight (rs4986938) of ESR2.
These findings support a role for estrogen and its major brain receptors in modulating susceptibility to AD in women.
PMCID: PMC3250648  PMID: 22156442
Estrogen; Estrogen receptor-beta; Down syndrome; Alzheimer's disease
14.  Variants in CYP17 and CYP19 Cytochrome P450 genes are associated with onset of Alzheimer’s disease in women with Down syndrome 
Journal of Alzheimer's Disease  2012;28(3):601-612.
CYP17and CYP19 are involved in the peripheral synthesis of estrogens, and polymorphisms in CYP17 and CYP19 have been associated with increased risk of estrogen-related disorders. Women with Down syndrome (DS) have early onset and high risk for Alzheimer’s disease (AD). We conducted a prospective community-based cohort study to examine the relationship between SNPs in CYP17 and CYP19 and cumulative incidence of AD, hormone levels and sex hormone binding globulin in women with DS. Two hundred and thirty-five women with DS, 31 to 67 years of age and nondemented at initial examination, were assessed for cognitive and functional abilities, behavioral/psychiatric conditions and health status at 14–20 month intervals over five assessment cycles. We genotyped these individuals for single-nucleotide polymorphisms (SNPs) in CYP17 and CYP19. Four SNPs in CYP17 were associated with a two and one half-fold increased risk of AD, independent of APOE genotype. Four SNPs in CYP19 were associated with a two-fold increased risk of AD, although three were significant only in those without an APOE ε4 allele. Further, carrying high risk alleles in both CYP17 and CYP19 was associated with an almost four-fold increased risk of AD (OR=3.8, 95% CI, 1.6–9.5) and elevated sex hormone binding globulin in postmenopausal women. The main effect of the CYP17 and CYP19 variants was to decrease the age at onset. These findings suggest that genes contributing to estrogen bioavailability influence risk of AD in women with DS.
PMCID: PMC3276705  PMID: 22057025
Estrogen; Down syndrome; Alzheimer’s disease; CYP17; CYP19; aromatase; genetics
15.  Molecular biology of cancer-associated fibroblasts: can these cells be targeted in anti-cancer therapy? 
It is increasingly recognized that the non-neoplastic stromal compartment in most solid cancers plays an active role in tumor proliferation, invasion and metastasis. Cancer associated fibroblasts (CAFs) are one of the most abundant cell types in the tumor stroma, and these cells are pro-tumorigenic. Evidence that CAFs are epigenetically and possibly also genetically distinct from normal fibroblasts is beginning to define these cells as potential targets of anti-cancer therapy. Here, we review the cell of origin and molecular biology of CAFs, arguing that such knowledge provides a rational basis for designing therapeutic strategies to coordinately and synergistically target both the stromal and malignant epithelial component of human cancers.
PMCID: PMC3531978  PMID: 19840860
16.  Epigenomic insights into common disease 
Genome Medicine  2011;3(11):71.
A report on the Wellcome Trust Scientific Conference 'Epigenomics of Common Diseases', Hinxton, Cambridge, UK, September 13-16, 2011.
PMCID: PMC3308026  PMID: 22085423
17.  Polymorphisms in HSD17B1: Early Onset and Increased Risk of Alzheimer's Disease in Women with Down Syndrome 
Background/Aims. Genetic variants that affect estrogen activity may influence the risk of Alzheimer's disease (AD). In women with Down syndrome, we examined the relation of polymorphisms in hydroxysteroid-17beta-dehydrogenase (HSD17B1) to age at onset and risk of AD. HSD17B1 encodes the enzyme 17β-hydroxysteroid dehydrogenase (HSD1), which catalyzes the conversion of estrone to estradiol. Methods. Two hundred and thirty-eight women with DS, nondemented at baseline, 31–78 years of age, were followed at 14–18-month intervals for 4.5 years. Women were genotyped for 5 haplotype-tagging single-nucleotide polymorphisms (SNPs) in the HSD17B1 gene region, and their association with incident AD was examined. Results. Age at onset was earlier, and risk of AD was elevated from two- to threefold among women homozygous for the minor allele at 3 SNPs in intron 4 (rs676387), exon 6 (rs605059), and exon 4 in COASY (rs598126). Carriers of the haplotype TCC, based on the risk alleles for these three SNPs, had an almost twofold increased risk of developing AD (hazard ratio = 1.8, 95% CI, 1.1–3.1). Conclusion. These findings support experimental and clinical studies of the neuroprotective role of estrogen.
PMCID: PMC3310186  PMID: 22474448
18.  Bone marrow-derived myofibroblasts contribute to the mesenchymal stem cell niche and promote tumor growth 
Cancer cell  2011;19(2):257-272.
Carcinoma associated fibroblasts (CAFs) that express α-smooth-muscle-actin (αSMA) contribute to cancer progression, but their precise origin and role is unclear. Using mouse models of inflammation-induced gastric cancer, we show that at least 20% of CAFs originate from bone marrow (BM) and derive from mesenchymal stem cells (MSCs). αSMA+ myofibroblasts (MF) are niche cells normally present in BM and increase markedly during cancer progression. MSC-derived CAFs that are recruited to the dysplastic stomach express IL-6, Wnt5α and BMP4, show DNA-hypomethylation, and promote tumor growth. Moreover, CAFs are generated from MSCs and are recruited to the tumor in TGF-β- and SDF-1α-dependent manner. Carcinogenesis therefore involves expansion and relocation of BM-niche cells to the tumor to create a niche to sustain cancer progression.
PMCID: PMC3060401  PMID: 21316604
Tumor microenvironment; Stem Cells; Bone Marrow-derived Cells (BMDC); MSC; CAF; MF; Carcinogenesis
19.  Allele-specific DNA methylation: beyond imprinting 
Human Molecular Genetics  2010;19(R2):R210-R220.
Allele-specific DNA methylation (ASM) and allele-specific gene expression (ASE) have long been studied in genomic imprinting and X chromosome inactivation. But these types of allelic asymmetries, along with allele-specific transcription factor binding (ASTF), have turned out to be far more pervasive—affecting many non-imprinted autosomal genes in normal human tissues. ASM, ASE and ASTF have now been mapped genome-wide by microarray-based methods and NextGen sequencing. Multiple studies agree that all three types of allelic asymmetries, as well as the related phenomena of expression and methylation quantitative trait loci, are mostly accounted for by cis-acting regulatory polymorphisms. The precise mechanisms by which this occurs are not yet understood, but there are some testable hypotheses and already a few direct clues. Future challenges include achieving higher resolution maps to locate the epicenters of cis-regulated ASM, using this information to test mechanistic models, and applying genome-wide maps of ASE/ASM/ASTF to pinpoint functional regulatory polymorphisms influencing disease susceptibility.
PMCID: PMC2953749  PMID: 20855472
20.  The caBIG® Life Science Business Architecture Model 
Bioinformatics  2011;27(10):1429-1435.
Motivation: Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG®) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research.
Results: LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model's current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases.
Availability and Implementation: The LS BAM is freely available as UML, PDF and HTML (
Supplementary information: Supplementary data) are avaliable at Bioinformatics online.
PMCID: PMC3087952  PMID: 21450709
21.  Altered PET Functional Brain Responses in Cognitively Intact Elderly Persons at Risk for Alzheimer Disease (Carriers of the ε4 Allele) 
Few previous studies have investigated the association between APOE genotype and brain activation during performance of cognitive tasks in healthy middle-aged and elderly subjects, and the results have been mixed. The authors investigated APOE-mediated differential brain activation in a group of healthy elderly subjects.
Using H2 15O positron emission tomography (PET), they imaged 32 healthy subjects (26 non-ε4 carriers and 6 ε4 carriers) performing a serial shape-recognition memory task under two conditions: Simple Demand (SD), in which one shape was presented in each study trial, and Titrated Demand (TD), in which study list length was adjusted so that each subject recognized words at approximately 75% accuracy. Multiple-regression analyses were performed, with the “activation” difference (TD–SD PET counts) as the dependent variable and the APOE genotype (presence versus absence of the ε4 allele) as the independent variable.
Compared with non-carriers, ε4 carriers exhibited significantly decreased TD–SD activation differences in the left superior temporal, right superior frontal, left postcental, left precuneus, and posterior cingulate gyrus because ε4 carriers (versus non-carriers) showed increased activation during the SD and decreased activation during the TD condition.
Patterns of brain activation during a nonverbal memory task differed as a function of APOE genotype and, therefore, of genetic risk for Alzheimer disease (AD). Differences in activation were not a reflection of task difficulty, but indicate memory-related altered cognitive processing. Brain regions with decreased activation in the ε4 subjects may result from subclinical incipient AD pathology and/or APOE-related neurophysiologic heterogeneity.
PMCID: PMC3025285  PMID: 15545327
22.  Altered DNA Methylation in Leukocytes with Trisomy 21 
PLoS Genetics  2010;6(11):e1001212.
The primary abnormality in Down syndrome (DS), trisomy 21, is well known; but how this chromosomal gain produces the complex DS phenotype, including immune system defects, is not well understood. We profiled DNA methylation in total peripheral blood leukocytes (PBL) and T-lymphocytes from adults with DS and normal controls and found gene-specific abnormalities of CpG methylation in DS, with many of the differentially methylated genes having known or predicted roles in lymphocyte development and function. Validation of the microarray data by bisulfite sequencing and methylation-sensitive Pyrosequencing (MS-Pyroseq) confirmed strong differences in methylation (p<0.0001) for each of 8 genes tested: TMEM131, TCF7, CD3Z/CD247, SH3BP2, EIF4E, PLD6, SUMO3, and CPT1B, in DS versus control PBL. In addition, we validated differential methylation of NOD2/CARD15 by bisulfite sequencing in DS versus control T-cells. The differentially methylated genes were found on various autosomes, with no enrichment on chromosome 21. Differences in methylation were generally stable in a given individual, remained significant after adjusting for age, and were not due to altered cell counts. Some but not all of the differentially methylated genes showed different mean mRNA expression in DS versus control PBL; and the altered expression of 5 of these genes, TMEM131, TCF7, CD3Z, NOD2, and NPDC1, was recapitulated by exposing normal lymphocytes to the demethylating drug 5-aza-2′deoxycytidine (5aza-dC) plus mitogens. We conclude that altered gene-specific DNA methylation is a recurrent and functionally relevant downstream response to trisomy 21 in human cells.
Author Summary
Down syndrome (DS; trisomy 21) is caused by the gain of a single extra chromosome 21. However, the mechanisms by which this extra chromosome produces the medical abnormalities seen in DS, including not only mental retardation but also susceptibility to autoimmune diseases and recurrent infections, are still not understood. DNA methylation is a mechanism that might contribute to these abnormalities. To test this possibility, we profiled DNA methylation in white blood cells from adults with DS and normal controls and found recurrent abnormalities of gene methylation in DS, with several of the differentially methylated genes having roles in blood cells. Among the genes with hypo- or hyper-methylation in white blood cells or purified T-lymphocytes from adults with DS, compared to these same types of cells from normal adults, were TMEM131, TCF7, CD3Z, SH3BP2, EIF4E, SUMO3, CPT1B, NOD2/CARD15, NPDC1, and PLD6. Several of these genes showed not only different methylation but also different expression in DS versus control blood cells, which was recapitulated by exposing normal white blood cells to a demethylating drug. These findings show that altered DNA methylation of a specific group of genes is a fundamental cellular response to the gain of an extra chromosome 21 in humans. The abnormally methylated genes identified here may contribute to immune system abnormalities in people with DS.
PMCID: PMC2987931  PMID: 21124956
23.  Methods in DNA methylation profiling 
Epigenomics  2009;1(2):331-345.
Metastable and somatically heritable patterns of DNA methylation provide an important level of genomic regulation. In this article, we review methods for analyzing these genome-wide epigenetic patterns and offer a perspective on the ever-expanding literature, which we hope will be useful for investigators who are new to this area. The historical aspects that we cover will be helpful in interpreting this literature and we hope that our discussion of the newest analytical methods will stimulate future progress. We emphasize that no single approach can provide a complete view of the overall methylome, and that combinations of several modalities applied to the same sample set will give the clearest picture. Given the unexpected epigenomic patterns and new biological principles, as well as new disease markers, that have been uncovered in recent studies, it is likely that important discoveries will continue to be made using genome-wide DNA methylation profiling.
PMCID: PMC2880494  PMID: 20526417
bisulfite sequencing; CpG island; differential methylation hybridization; DNA methylation; methylation profiling; methylated CpG island recovery assay; methylated DNA immunoprecipitation; methylation-sensitive SNP chip analysis; next-generation DNA sequencing
24.  Genome-Wide Divergence of DNA Methylation Marks in Cerebral and Cerebellar Cortices 
PLoS ONE  2010;5(6):e11357.
Emerging evidence suggests that DNA methylation plays an expansive role in the central nervous system (CNS). Large-scale whole genome DNA methylation profiling of the normal human brain offers tremendous potential in understanding the role of DNA methylation in brain development and function.
Methodology/Significant Findings
Using methylation-sensitive SNP chip analysis (MSNP), we performed whole genome DNA methylation profiling of the prefrontal, occipital, and temporal regions of cerebral cortex, as well as cerebellum. These data provide an unbiased representation of CpG sites comprising 377,509 CpG dinucleotides within both the genic and intergenic euchromatic region of the genome. Our large-scale genome DNA methylation profiling reveals that the prefrontal, occipital, and temporal regions of the cerebral cortex compared to cerebellum have markedly different DNA methylation signatures, with the cerebral cortex being hypermethylated and cerebellum being hypomethylated. Such differences were observed in distinct genomic regions, including genes involved in CNS function. The MSNP data were validated for a subset of these genes, by performing bisulfite cloning and sequencing and confirming that prefrontal, occipital, and temporal cortices are significantly more methylated as compared to the cerebellum.
These findings are consistent with known developmental differences in nucleosome repeat lengths in cerebral and cerebellar cortices, with cerebrum exhibiting shorter repeat lengths than cerebellum. Our observed differences in DNA methylation profiles in these regions underscores the potential role of DNA methylation in chromatin structure and organization in CNS, reflecting functional specialization within cortical regions.
PMCID: PMC2893206  PMID: 20596539
Cancer research  2008;68(23):9900-9908.
Global loss of methylation has long been recognized as a feature of the malignant epithelial component in human carcinomas. Here we show evidence for this same type of epigenetic alteration in cancer-associated stromal myofibroblasts. We used methylation-sensitive SNP array analysis (MSNP) to profile DNA methylation in early passage cultures of stromal myofibroblasts isolated from human gastric cancers. The MSNP data indicated widespread loss of methylation in these cells, with rare focal gains of methylation, conclusions that were independently validated by bisulfite sequencing and by a methylation-sensitive cytosine incorporation assay. Immunohistochemistry (IHC) using anti-methylcytosine (anti-methyl-C) in a series of gastrectomy specimens showed frequent loss of methylation in nuclei of both the malignant epithelial cells and the alpha smooth muscle actin (ASMA)-positive stromal myofibroblasts of both intestinal type and diffuse carcinomas. We confirmed this phenomenon and established its onset at the stage of non-invasive dysplastic lesions by IHC for anti-methyl-C in a transgenic mouse model of multi-stage gastric carcinogenesis. These findings indicate similar general classes of epigenetic alterations in carcinoma cells and their accompanying reactive stromal cells and add to accumulating evidence for biological differences between normal and cancer-associated myofibroblasts.
PMCID: PMC2670548  PMID: 19047171

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