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1.  Environmental Exposures, Epigenetics and Cardiovascular Disease 
Purpose of the Review
Epigenetic modifications are heritable alterations of the genome, which can govern gene expression without altering the DNA sequence. The purpose of this review is to render an overview of the possible mechanisms of epigenetic regulation of gene expression in response to environmental pollutants leading to cardiovascular diseases (CVD).
Recent Findings
An era of cataloging epigenetic marks of the various diseased states has recently commenced, including those within the genes responsible for atherosclerosis, ischemia, hypertension and heart failure. From varied study approaches directed either towards the general understanding of the key pathway regulatory genes, or sampling population cohorts for global and gene-specific changes, it has been possible to identify several epigenetic signatures of environmental exposure relevant to CVD. Signatures of epigenetic dysregulation can be detected in peripheral blood samples, even within few hours of environmental exposure. However, the field now faces the demand for thorough, systematic, rationalized approaches to establish the relation of an exposure-driven epigenetic changes to clinical outcomes, by using sophisticated and reliable research designs and tools.
Summary
An understanding of chromatin remodeling in response to environmental stimuli conducive to CVD is emerging, with the promise of novel diagnostic and therapeutic candidates.
doi:10.1097/MCO.0b013e328354bf5c
PMCID: PMC3742092  PMID: 22669047
Environment; Cardiovascular; Epigenetics; DNA methylation; Histone modifications; Biomarkers
2.  Twins for epigenetic studies of human aging and development 
Ageing research reviews  2012;12(1):182-187.
Most of the complex traits including aging phenotypes are caused by the interaction between genome and environmental conditions and the interface of epigenetics may be a central mechanism. Although modern technologies allow us high-throughput profiling of epigenetic patterns already at genome level, our understanding of genetic and environmental influences on the epigenetic processes remains limited. Twins are of special interest for genetic studies due to their genetic similarity and rearing-environment sharing. The classical twin design has made a great contribution in dissecting the genetic and environmental contributions to human diseases and complex traits. In the era of functional genomics, the valuable sample of twins is helping to bridge the gap between gene activity and the environments through epigenetic mechanisms unlimited by DNA sequence variations. We propose toextend the classical twin design to studythe aging–related molecular epigenetic phenotypes and link them with environmental exposures especially early life events. Different study designs and application issues will be highlighted and novel approaches introduced with aim at making uses of twins in assessing the environmental impact on epigenetic changes during development and in the aging process.
doi:10.1016/j.arr.2012.06.004
PMCID: PMC3509237  PMID: 22750314
twins; aging; epigenetics; environments; genomics
3.  Epigenetic Aspects of Posttraumatic Stress Disorder 
Disease markers  2011;30(2-3):77-87.
Development of psychiatric diseases such as posttraumatic stress disorder (PTSD) invokes, as with most complex diseases, both genetic and environmental factors. The era of genome-wide high throughput technologies has sparked the initiation of genotype screenings in large cohorts of diseased and control individuals, but had limited success in identification of disease causing genetic variants. It has become evident that these efforts at the genomic level need to be complemented with endeavours in elucidating the proteome, transcriptome and epigenetic profiles. Epigenetics is attractive in particular because there is accumulating evidence that the lasting impact of adverse life events is reflected in certain covalent modifications of the chromatin.
In this review, we outline the characteristics of PTSD as a stress-related disease and survey recent developments revealing epigenetic aspects of stress-related disorders in general. There is also increasing direct evidence for gene programming and epigenetic components in PTSD. Finally, we discuss treatment options in the light of recent discoveries of epigenetic mechanisms of psychotropic drugs.
doi:10.3233/DMA-2011-0749
PMCID: PMC3825244  PMID: 21508512
4.  Genetic and Epigenetic Changes in Human Prostate Cancer 
Acquired or inherited genetic alterations either alone or in combination with epigenetic alterations are associated with prostate carcinogenesis and its progression toward advance metastatic or castration-resistant disease. A major objective of translational cancer research in post-genome era is to discover the repertoire of genetic and epigenetic variations associated with prostate cancer. Genome-wide association studies have been at least partially successful in identifying potential germline polymorphisms and allelic imbalances such as microsatellite instability and loss of heterozygosity associated with prostate cancer susceptibility. Epigenetic mechanisms such as DNA hyper- or hypomethylation and histone modifications are reversible genetic alterations which allow stable inheritance of cellular phenotypes without any changes in the DNA sequence or quantity. Epigenetic modifications can potentially be used for the molecular classification, detection, and risk assessment in prostate cancer. Chemical inhibitors of DNA methyltransferases and histone deacetylases have been used in different clinical trials and hold promise as novel chemotherapeutics to be effective alone or in combination with other therapeutic interventions in prostate cancer.
PMCID: PMC3371912  PMID: 22737441
Genetics; Epigenetics; Genome; Somatic; Germline; Prostate Cancer
5.  An updated review of gastric cancer in the next-generation sequencing era: Insights from bench to bedside and vice versa 
Gastric cancer (GC) is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide. There is an increasing understanding of the roles that genetic and epigenetic alterations play in GCs. Recent studies using next-generation sequencing (NGS) have revealed a number of potential cancer-driving genes in GC. Whole-exome sequencing of GC has identified recurrent somatic mutations in the chromatin remodeling gene ARID1A and alterations in the cell adhesion gene FAT4, a member of the cadherin gene family. Mutations in chromatin remodeling genes (ARID1A, MLL3 and MLL) have been found in 47% of GCs. Whole-genome sequencing and whole-transcriptome sequencing analyses have also discovered novel alterations in GC. Recent studies of cancer epigenetics have revealed widespread alterations in genes involved in the epigenetic machinery, such as DNA methylation, histone modifications, nucleosome positioning, noncoding RNAs and microRNAs. Recent advances in molecular research on GC have resulted in the introduction of new diagnostic and therapeutic strategies into clinical settings. The anti-human epidermal growth receptor 2 (HER2) antibody trastuzumab has led to an era of personalized therapy in GC. In addition, ramucirumab, a monoclonal antibody targeting vascular endothelial growth factor receptor (VEGFR)-2, is the first biological treatment that showed survival benefits as a single-agent therapy in patients with advanced GC who progressed after first-line chemotherapy. Using NGS to systematically identify gene alterations in GC is a promising approach with remarkable potential for investigating the pathogenesis of GC and identifying novel therapeutic targets, as well as useful biomarkers. In this review, we will summarize the recent advances in the understanding of the molecular pathogenesis of GC, focusing on the potential use of these genetic and epigenetic alterations as diagnostic biomarkers and novel therapeutic targets.
doi:10.3748/wjg.v20.i14.3927
PMCID: PMC3983448  PMID: 24744582
Next-generation sequencing; Microsatellite instability; MicroRNA; Epigenetic field defect; Gastric washes; Insulin-like growth factor 1 receptor
6.  Medulloblastoma biology in the post-genomic era 
Future oncology (London, England)  2012;8(12):1597-1604.
Medulloblastomas, the most common malignant pediatric brain tumors, are comprised of four molecularly distinct subtypes. However, treatment has yet to exploit these molecular vulnerabilities. Three recent studies sequenced a total of 310 primary tumors and identified that two of the four medulloblastoma subtypes are concomitantly associated with subtype-specific mutations as previously characterized. In contrast, the overwhelming majority of mutations occurred only once in the entire cohort and just 12 genes were recurrently mutated with statistical significance. Perturbations in epigenetic regulation are emerging as a unifying theme in cancer and similarly recurring mutations in epigenetic mechanisms were distributed across all subtypes in medulloblastoma. Designing targeted therapies to such a molecularly diverse disease in the post-genomic era presents new challenges. This will require novel methods to link these nonrecurrent mutations into pathways, and preclinical models that faithfully recapitulate patient driver events. Presently, medulloblastoma reinforces epigenetic mechanisms as a tantalizing therapeutic target in cancers.
doi:10.2217/fon.12.151
PMCID: PMC3602901  PMID: 23231521
cerebellum; chromatin; epigenetics; epigenomics; medulloblastoma; Swi/Snf; systems biology
7.  Methylation and worker reproduction in the bumble-bee (Bombus terrestris) 
Insects are at the dawn of an epigenetics era. Numerous social insect species have been found to possess a functioning methylation system, previously not thought to exist in insects. Methylation, an epigenetic tag, may be vital for the sociality and division of labour for which social insects are renowned. In the bumble-bee Bombus terrestris, we found methylation differences between the genomes of queenless reproductive workers and queenless non-reproductive workers. In a follow up experiment, queenless workers whose genomes had experimentally altered methylation were more aggressive and more likely to develop ovaries compared with control queenless workers. This shows methylation is important in this highly plastic reproductive division of labour. Methylation is an epigenetic tag for genomic imprinting (GI). It is intriguing that the main theory to explain the evolution of GI predicts that GI should be important in this worker reproduction behaviour.
doi:10.1098/rspb.2013.2502
PMCID: PMC4027386  PMID: 24523266
intragenomic conflict; epigenetics; worker male production; methylation-sensitive AFLP
8.  Metabostemness: A New Cancer Hallmark 
Frontiers in Oncology  2014;4:262.
The acquisition of and departure from stemness in cancer tissues might not only be hardwired by genetic controllers, but also by the pivotal regulatory role of the cellular metabotype, which may act as a “starter dough” for cancer stemness traits. We have coined the term metabostemness to refer to the metabolic parameters causally controlling or functionally substituting the epitranscriptional orchestration of the genetic reprograming that redirects normal and tumor cells toward less-differentiated cancer stem cell (CSC) cellular states. Certain metabotypic alterations might operate as pivotal molecular events rendering a cell of origin susceptible to epigenetic rewiring required for the acquisition of aberrant stemness and, concurrently, of refractoriness to differentiation. The metabostemness attribute can remove, diminish, or modify the nature of molecular barriers present in Waddington’s epigenetic landscapes, thus allowing differentiated cells to more easily (re)-enter into CSC cellular macrostates. Activation of the metabostemness trait can poise cells with chromatin states competent for rapid dedifferentiation while concomitantly setting the idoneous metabolic stage for later reprograming stimuli to finish the journey from non-cancerous into tumor-initiating cells. Because only a few permitted metabotypes will be compatible with the operational properties owned by CSC cellular states, the metabostemness property provides a new framework through which to pharmacologically resolve the apparently impossible problem of discovering drugs aimed to target the molecular biology of the cancer stemness itself. The metabostemness cancer hallmark generates a shifting oncology theory that should guide a new era of metabolo-epigenetic cancer precision medicine.
doi:10.3389/fonc.2014.00262
PMCID: PMC4179679  PMID: 25325014
stemness; metabolism; reprograming; cancer stem cells; oncometabolites; Waddington; epigenetic landscapes
9.  Risk of Death and Myocardial Infarction in Patients with Peripheral Arterial Disease Undergoing Percutaneous Coronary Intervention: From the National Heart, Lung and Blood Institute Dynamic Registry 
The American journal of cardiology  2011;107(7):959-964.
Patients with peripheral arterial disease (PAD) undergoing percutaneous coronary intervention (PCI) are at high risk for adverse cardiovascular events. Trends over time in outcomes with advances in PCI and medical therapy are unknown. We evaluated 866 patients with PAD in the National Heart, Lung, and Blood Institute (NHLBI) Dynamic Registry undergoing PCI according to treatment eras: the early bare metal stent (BMS) era (Wave 1: 1997-1998, n=180), the BMS era (Waves 2 and 3; 1999 and 2001-2002; n=339), and the drug-eluting stent (DES) era (Waves 4 and 5: 2004 and 2006; n=347). We compared in-hospital and 1-year outcomes by recruitment era. In-hospital coronary artery bypass graft surgery (CABG) rates were significantly lower in the later eras (3.9%, 0.9%, 0.6%, early BMS, BMS, and DES eras respectively, ptrend=0.005), and an increasing percentage of patients were discharged on aspirin, beta blockers, statins, and thienopyridines (all ptrend<0.001). Cumulative 1-year event rates in patients with PAD in the early BMS era, BMS era, and DES era of death were 13.7%, 10.5%, and 9.8% (ptrend = 0.21), of myocardial infarction (MI) were 9.8%, 8.8%, and 10.0% (ptrend = 0.95), and repeat revascularization were 26.8%, 21.0%, and 17.2% (ptrend = 0.008). The 1-year adjusted hazard ratios (HR) of adverse events in patients with PAD using the early BMS era as the reference are as follows: Death: BMS era HR=0.84 (95% CI 0.46-1.55, p=0.58) and DES era HR=1.35 (95% CI 0.71-2.56, p=0.36); MI: BMS era HR=0.89 (95% CI 0.48-1.66, p=0.72) and DES era HR=1.02 (95% CI 0.55-1.87, p=0.95); and repeat revascularization: BMS era HR=0.63 (95% CI 0.41-0.97, p=0.04) and DES era HR=0.46 (95% CI 0.29-0.73, p=0.001). In conclusion, despite significant improvements in medical therapy and a reduction in repeat revascularization over time, patients with PAD who undergo PCI have a persistent high rate of death and MI.
doi:10.1016/j.amjcard.2010.11.019
PMCID: PMC3071613  PMID: 21256469
Peripheral arterial disease; stents; catheterization
10.  Improved survival among HIV-infected patients after initiation of triple-drug antiretroviral regimens 
BACKGROUND: The efficacy of triple-drug antiretroviral regimens in the treatment of patients infected with HIV has been established in several randomized clinical trials. However, the effectiveness of these new regimens in patient populations outside clinical trials remain unproven. This study compared mortality and AIDS-free survival among HIV-infected patients in British Columbia who were treated with double- and triple-drug regimens. METHODS: The authors used a prospective, population-based cohort design to study a population of HIV-positive men and women 18 years or older for whom antiretroviral therapy was first prescribed between Oct. 1, 1994, and Dec. 31, 1996; all patients were from British Columbia. Rates of progression from the initiation of antiretroviral therapy to death or to diagnosis of primary AIDS were determined for patients who initially received an ERA-II regimen (2 nucleoside analogue reverse transcriptase inhibitors [NRTIs] including lamivudine or stavudine, or both) and for those who initially received an ERA-III regimen (triple-drug regimen consisting of 2 NRTIs and a protease inhibitor [indinavir, ritonavir or saquinavir] or a non-NRTI [nevirapine]). RESULTS: A total of 500 men and women (312 receiving an ERA-III regimen and 188 an ERA-III regimen) were eligible. Patients in the ERA-III group survived significantly longer than those in the ERA-II group. As of Dec. 31, 1997, 40 patients had died (35 in the ERA-II group and 5 in the ERA-III group), for a crude mortality rate of 8.0%. The cumulative mortality rates at 12 months were 7.4% (95% confidence interval [CI] 5.9% to 8.9%) for patients in the ERA-II group and 1.6% (95% CI 0.7% to 2.5%) for those in the ERA-III group (log rank p = 0.003). The likelihood of death was more than 3 times higher among patients in the ERA-II group (mortality risk ratio 3.82 [95% CI 1.48% to 9.84], p = 0.006). After adjustment for prophylaxis for Pneumocystis carinii pneumonia or Mycobacterium avium infection, AIDS diagnosis, CD4+ cell count, sex and age at initiation of therapy, the likelihood of death among patients in the ERA-II group was 3.21 times higher (95% CI 1.24 to 8.30, p = 0.016) than in the ERA-III group. Cumulative rates of progression to AIDS or death at 12 months were 9.6% (95% CI 7.7% to 11.5%) in the ERA-II group and 3.3% (95% CI 1.8% to 4.8%) in the ERA-III group (log rank p = 0.006). After adjustment for prognostic variables (prophylaxis for P. carinii pneumonia or M. avium infection, CD4+ cell count, sex and age at initiation of treatment), the likelihood of progression to AIDS or death at 12 months among patients in the ERA-II group was 2.37 times higher (95% CI 1.04 to 5.38, p = 0.040) than in the ERA-III group. INTERPRETATION: This population-based cohort study confirms that patients initially treated with a triple-drug antiretroviral regimen comprising 2 NRTIs plus protease inhibitor or a non-NRTI have a lower risk of morbidity and death than patients treated exclusively with 2 NRTIs.
PMCID: PMC1230111  PMID: 10102000
11.  MAOA promoter methylation and susceptibility to carotid atherosclerosis: role of familial factors in a monozygotic twin sample 
BMC Medical Genetics  2012;13:100.
Background
Atherosclerosis is a complex process involving both genetic and epigenetic factors. The monoamine oxidase A (MAOA) gene regulates the metabolism of key neurotransmitters and has been associated with cardiovascular risk factors. This study investigates whether MAOA promoter methylation is associated with atherosclerosis, and whether this association is confounded by familial factors in a monozygotic (MZ) twin sample.
Methods
We studied 84 monozygotic (MZ) twin pairs drawn from the Vietnam Era Twin Registry. Carotid intima-media thickness (IMT) was measured by ultrasound. DNA methylation in the MAOA promoter region was quantified by bisulfite pyrosequencing using genomic DNA isolated from peripheral blood leukocytes. The association between DNA methylation and IMT was first examined by generalized estimating equation, followed by matched pair analyses to determine whether the association was confounded by familial factors.
Results
When twins were analyzed as individuals, increased methylation level was associated with decreased IMT at four of the seven studied CpG sites. However, this association substantially reduced in the matched pair analyses. Further adjustment for MAOA genotype also considerably attenuated this association.
Conclusions
The association between MAOA promoter methylation and carotid IMT is largely explained by familial factors shared by the twins. Because twins reared together share early life experience, which may leave a long-lasting epigenetic mark, aberrant MAOA methylation may represent an early biomarker for unhealthy familial environment. Clarification of familial factors associated with DNA methylation and early atherosclerosis will provide important information to uncover clinical correlates of disease.
doi:10.1186/1471-2350-13-100
PMCID: PMC3532355  PMID: 23116433
DNA methylation; MAOA; Carotid atherosclerosis; Monozygotic twins; Familial factors
12.  The landscape for epigenetic/epigenomic biomedical resources 
Epigenetics  2012;7(9):982-986.
Recent advances in molecular biology and computational power have seen the biomedical sector enter a new era, with corresponding development of Bioinformatics as a major discipline. Generation of enormous amounts of data has driven the need for more advanced storage solutions and shared access through a range of public repositories. The number of such biomedical resources is increasing constantly and mining these large and diverse data sets continues to present real challenges. This paper attempts a general overview of currently available resources, together with remarks on their data mining and analysis capabilities. Of interest here is the recent shift in focus from genetic to epigenetic/epigenomic research and the emergence and extension of resource provision to support this both at local and global scale. Biomedical text and numerical data mining are both considered, the first dealing with automated methods for analyzing research content and information extraction, and the second (broadly) with pattern recognition and prediction. Any summary and selection of resources is inherently limited, given the spectrum available, but the aim is to provide a guideline for the assessment and comparison of currently available provision, particularly as this relates to epigenetics/epigenomics.
doi:10.4161/epi.21493
PMCID: PMC3515018  PMID: 22874136
biomedical resource; data mining; epigenetics; epigenomics; methylation; primary database; secondary database
13.  MGMT Methylation Status: The Advent of Stratified Therapy in Glioblastoma? 
Disease Markers  2007;23(1-2):97-104.
Glioblastomas are the most malignant gliomas with median survival times of only 15 months despite modern therapies. All standard treatments are palliative. Pathogenetic factors are diverse, hence, stratified treatment plans are warranted considering the molecular heterogeneity among these tumors. However, most patients are treated with "one fits all" standard therapies, many of them with minor response and major toxicities. The integration of clinical and molecular information, now becoming available using new tools such as gene arrays, proteomics, and molecular imaging, will take us to an era where more targeted and effective treatments may be implemented.
A first step towards the design of such therapies is the identification of relevant molecular mechanisms driving the aggressive biological behavior of glioblastoma. The accumulation of diverse aberrations in regulatory processes enables tumor cells to bypass the effects of most classical therapies available. Molecular alterations underlying such mechanisms comprise aberrations on the genetic level, such as point mutations of distinct genes, or amplifications and deletions, while others result from epigenetic modifications such as aberrant methylation of CpG islands in the regulatory sequence of genes. Epigenetic silencing of the MGMT gene encoding a DNA repair enzyme was recently found to be of predictive value in a randomized clinical trial for newly diagnosed glioblastoma testing the addition of the alkylating agent temozolomide to standard radiotherapy. Determination of the methylation status of the MGMT promoter may become the first molecular diagnostic tool to identify patients most likely to respond that will allow individually tailored therapy in glioblastoma.
To date, the test for the MGMT-methylation status is the only tool available that may direct the choice for alkylating agents in glioblastoma patients, but many others may hopefully become part of an arsenal to stratify patients to respective targeted therapies within the next years.
doi:10.1155/2007/159242
PMCID: PMC3851641  PMID: 17325429
Glioblastoma; predictive factors; personalized therapy; targeted therapy; MGMT
14.  A symbiotic liaison between the genetic and epigenetic code 
Frontiers in Genetics  2014;5:113.
With rapid advances in sequencing technologies, we are undergoing a paradigm shift from hypothesis- to data-driven research. Genome-wide profiling efforts have given informative insights into biological processes; however, considering the wealth of variation, the major challenge still remains in their meaningful interpretation. In particular sequence variation in non-coding contexts is often challenging to interpret. Here, data integration approaches for the identification of functional genetic variability represent a possible solution. Exemplary, functional linkage analysis integrating genotype and expression data determined regulatory quantitative trait loci and proposed causal relationships. In addition to gene expression, epigenetic regulation and specifically DNA methylation was established as highly valuable surrogate mark for functional variance of the genetic code. Epigenetic modification has served as powerful mediator trait to elucidate mechanisms forming phenotypes in health and disease. Particularly, integrative studies of genetic and DNA methylation data have been able to guide interpretation strategies of risk genotypes, but also proved their value for physiological traits, such as natural human variation and aging. This Review seeks to illustrate the power of data integration in the genomic era exemplified by DNA methylation quantitative trait loci. However, the model is further extendable to virtually all traceable molecular traits.
doi:10.3389/fgene.2014.00113
PMCID: PMC4013453  PMID: 24822056
DNA methylation quantitaive trait loci; DNA methylation; GWAS; EWAS; epigenetic regulation
15.  Throwing the Cancer Switch 
Nature reviews. Cancer  2010;10(10):669-682.
Preface
The discovery that cancer can be governed above and beyond the level of our DNA presents a new era for designing therapies that reverse the epigenetic state of a tumor cell. Understanding how altered chromatin dynamics leads to malignancy is essential for controlling tumor cells while sparing normal cells. Polycomb and trithorax group proteins are evolutionarily conserved and maintain chromatin in the “off” or “on” state, thereby preventing or promoting gene expression, respectively. Recent work highlights the dynamic interplay between these opposing classes of proteins, providing new avenues for understanding how these epigenetic regulators function in tumorigenesis.
doi:10.1038/nrc2931
PMCID: PMC4068012  PMID: 20865010
16.  Maternal diet: a modulator for epigenomic regulation during development in nonhuman primates and humans 
The importance of diet in health and disease has been well characterized in the past decades. Although the earlier focus of diet research was in the context of undernutrition and the importance of adequate nutrient intake to prevent malnutrition, in the current era of epidemic obesity the focus of our efforts has evolved toward understanding the effects of excess caloric intake. The current surge in childhood obesity rates suggests a correlation of maternal metabolic syndrome and obesity with programming of the fetal epigenome for metabolic diseases later in life. Alterations of the fetal genome, epigenome and metabolome have been well documented in cases of maternal malnutrition, including both overnutrition and undernutrition. It is of great interest and importance to understand how these divergent maternal factors regulate/program the fetus for metabolic diseases, and we and others have observed that epigenetic modifications to the fetal and placental epigenome accompany these reprogramming events. The following review summarizes recent studies on the effects of maternal diet and obesity on fetal epigenetics contributing to adult diseases later in life by taking advantage of state-of-the-art genomic, epigenomic and metagenomic techniques in nonhuman primate model systems.
doi:10.1038/ijosup.2012.16
PMCID: PMC4089706  PMID: 25018872
high-fat diet; DOHaD; nonhuman primate; epigenetics
17.  The Role of the Toxicologic Pathologist in the Post-Genomic Era# 
Journal of Toxicologic Pathology  2013;26(2):105-110.
An era can be defined as a period in time identified by distinctive character, events, or practices. We are now in the genomic era. The pre-genomic era: There was a pre-genomic era. It started many years ago with novel and seminal animal experiments, primarily directed at studying cancer. It is marked by the development of the two-year rodent cancer bioassay and the ultimate realization that alternative approaches and short-term animal models were needed to replace this resource-intensive and time-consuming method for predicting human health risk. Many alternatives approaches and short-term animal models were proposed and tried but, to date, none have completely replaced our dependence upon the two-year rodent bioassay. However, the alternative approaches and models themselves have made tangible contributions to basic research, clinical medicine and to our understanding of cancer and they remain useful tools to address hypothesis-driven research questions. The pre-genomic era was a time when toxicologic pathologists played a major role in drug development, evaluating the cancer bioassay and the associated dose-setting toxicity studies, and exploring the utility of proposed alternative animal models. It was a time when there was shortage of qualified toxicologic pathologists. The genomic era: We are in the genomic era. It is a time when the genetic underpinnings of normal biological and pathologic processes are being discovered and documented. It is a time for sequencing entire genomes and deliberately silencing relevant segments of the mouse genome to see what each segment controls and if that silencing leads to increased susceptibility to disease. What remains to be charted in this genomic era is the complex interaction of genes, gene segments, post-translational modifications of encoded proteins, and environmental factors that affect genomic expression. In this current genomic era, the toxicologic pathologist has had to make room for a growing population of molecular biologists. In this present era newly emerging DVM and MD scientists enter the work arena with a PhD in pathology often based on some aspect of molecular biology or molecular pathology research. In molecular biology, the almost daily technological advances require one’s complete dedication to remain at the cutting edge of the science. Similarly, the practice of toxicologic pathology, like other morphological disciplines, is based largely on experience and requires dedicated daily examination of pathology material to maintain a well-trained eye capable of distilling specific information from stained tissue slides - a dedicated effort that cannot be well done as an intermezzo between other tasks. It is a rare individual that has true expertise in both molecular biology and pathology. In this genomic era, the newly emerging DVM-PhD or MD-PhD pathologist enters a marketplace without many job opportunities in contrast to the pre-genomic era. Many face an identity crisis needing to decide to become a competent pathologist or, alternatively, to become a competent molecular biologist. At the same time, more PhD molecular biologists without training in pathology are members of the research teams working in drug development and toxicology. How best can the toxicologic pathologist interact in the contemporary team approach in drug development, toxicology research and safety testing? Based on their biomedical training, toxicologic pathologists are in an ideal position to link data from the emerging technologies with their knowledge of pathobiology and toxicology. To enable this linkage and obtain the synergy it provides, the bench-level, slide-reading expert pathologist will need to have some basic understanding and appreciation of molecular biology methods and tools. On the other hand, it is not likely that the typical molecular biologist could competently evaluate and diagnose stained tissue slides from a toxicology study or a cancer bioassay. The post-genomic era: The post-genomic era will likely arrive approximately around 2050 at which time entire genomes from multiple species will exist in massive databases, data from thousands of robotic high throughput chemical screenings will exist in other databases, genetic toxicity and chemical structure-activity-relationships will reside in yet other databases. All databases will be linked and relevant information will be extracted and analyzed by appropriate algorithms following input of the latest molecular, submolecular, genetic, experimental, pathology and clinical data. Knowledge gained will permit the genetic components of many diseases to be amenable to therapeutic prevention and/or intervention. Much like computerized algorithms are currently used to forecast weather or to predict political elections, computerized sophisticated algorithms based largely on scientific data mining will categorize new drugs and chemicals relative to their health benefits versus their health risks for defined human populations and subpopulations. However, this form of a virtual toxicity study or cancer bioassay will only identify probabilities of adverse consequences from interaction of particular environmental and/or chemical/drug exposure(s) with specific genomic variables. Proof in many situations will require confirmation in intact in vivo mammalian animal models. The toxicologic pathologist in the post-genomic era will be the best suited scientist to confirm the data mining and its probability predictions for safety or adverse consequences with the actual tissue morphological features in test species that define specific test agent pathobiology and human health risk.
doi:10.1293/tox.26.105
PMCID: PMC3695332  PMID: 23914052
genomic era; history of toxicologic pathology; molecular biology
18.  Changing Pattern of Organ Donation and Utilization in the USA 
Background: Organ transplantation has proven highly effective in the treatment of various forms of end-stage organ failure. However, organ shortage is still the greatest challenge facing the field of organ transplantation.
Objective: To assess the pattern of organ donation and utilization during the past decade in the USA.
Methods: We studied OPTN/UNOS database for organ donation between January 2000 and December 2009. The retrieved records were then categorized into two time periods—from January 2000 to December 2004 (era 1), and from January 2005 to December 2009 (era 2).
Results: There were 65,802 living and 71,401 deceased donors in the US from 2000 to 2009, including 66,518 (93.2%) brain-dead donors and 4,883 (6.8%) donation after cardiac death. Comparing two periods—from January 2000 to December 2004 (era 1) and from January 2005 to December 2009 (era 2), the number of deceased donors increased by 25% from 31,692 to 39,709 and living donors decreased by 7.6%. Donation after cardiac death increased from 3.5% to 9.3%. The portion of donors older than 64 years increased from 6.9% in era 1 to 11.3% in era 2 (p=0.03). The number of donors with a body mass index of >35 kg/m2 was also increased from 6.8% to 11.2%. A significant increase in the incidence of cardiovascular/cerebrovascular as cause of death was also noted from 38.1% in era 1 to 56.1% in era 2 (p<0.001), as was a corresponding decrease in the incidence of death due to head trauma (34.9% vs. 48.8%). The overall discard rate also increased by 41% from 13,411 in era 1 to 19,516 in era 2. This increase in discards was especially more prominent in donation after cardiac death group which rose by 374% from 440 in era 1 to 2,089 in era 2. The discard rate for livers and kidneys increased by 31% and 68%, respectively, comparing era 1 and era 2. We noted a 78% increase for discarded donation after cardiac death livers and 1,210% for discarded donation after cardiac death kidneys.
Conclusion: We detected significant changes in the make-up of the donor pool over the past decade in the US. Over time, donor characteristics have changed with increased numbers of elderly donors and donors with comorbidities, especially donors who died of cardiovascular/cerebrovascular disease. The incidence of donation after cardiac death has increased significantly; brain-dead donors have only increased slightly and living donors have decreased. As the result, the discard rates have increased. The transplant community and policy makers should consider every precaution to safeguard the donor pool and prevent the decay of organ quality in favor of quantity.
PMCID: PMC4089300  PMID: 25013640
Organ transplantation; End-stage organ failure; Brain-dead donor; Living donors
19.  Population-based outcomes after brain radiotherapy in patients with brain metastases from breast cancer in the Pre-Trastuzumab and Trastuzumab eras 
Purpose
To evaluate the survival of patients with human epidermal growth factor receptor 2 (HER2) positive and negative metastatic breast cancer irradiated for brain metastases before and after the availability of trastuzumab (T).
Materials and methods
Women diagnosed with brain metastasis from breast cancer in two eras between 2000 and 2007 (T-era, n = 441) and 1986 to 1992 (PreT-era, n = 307), treated with whole brain radiotherapy (RT) were identified. In the T-era, HER2 testing was part of routine clinical practice, and in the preT-era 128/307 (42%) cases had HER2 testing performed retrospectively on tissue microarrays. Overall survival (OS) was estimated using the Kaplan-Meier method and comparisons between eras used log-rank tests.
Results
In the preT- and T-era cohorts, the rate of HER2 positivity was 40% (176/441) and 26% (33/128) (p < 0.001). The median time from diagnosis to brain RT was longer in the preT-era (3.3 years versus 2.3 years, p < 0.001). Survival after brain RT was improved in the T-era compared to the preT-era (1-year OS 26% versus 12%, p < 0.001). The 1-year OS rate for HER2 negative patients was 20% in both eras (p = 0.97). Among HER2 positive patients, the 1-year OS in the preT-era was 5% compared to 40% in the T-era (p < 0.001).
Conclusions
Distinct from patients with HER2 negative disease in whom no difference in survival after brain RT was observed over time, patients with HER2 positive brain metastases experienced significantly improved survival subsequent to the availability of trastuzumab.
doi:10.1186/1748-717X-8-12
PMCID: PMC3582534  PMID: 23302543
Breast cancer; Brain metastasis; Brain irradiation; Trastuzumab; HER2 status
20.  16S rRNA Is Bound to Era of Streptococcus pneumoniae 
Journal of Bacteriology  1999;181(17):5242-5249.
Era is an essential membrane-associated GTPase that is present in bacteria and mycoplasmas. Era appears to play an important role in the regulation of the bacterial cell cycle. In this study, we expressed the native and glutathione S-transferase (GST) fusion forms of Streptococcus pneumoniae Era in Escherichia coli and purified both proteins to homogeneity. We showed that RNA was copurified with the GST-Era protein of S. pneumoniae during affinity purification and remained associated with the protein after removal of the GST tag by thrombin cleavage. The thrombin-treated and untreated GST-Era proteins could bind and hydrolyze GTP and exhibited similar kinetic properties (dissociation constant [kD], Km, and Vmax). However, the native Era protein purified by using different chromatographic columns had a much lower GTPase activity than did GST-Era, although it had a similar kD. In addition, RNA was not associated with the protein. Purified GST-Era protein was shown to be present as high (600-kDa)- and low (120-kDa)-molecular-mass forms. The high-molecular-mass form of GST-Era was associated with RNA and exhibited a very high GTPase activity. Approximately 40% of purified GST-Era protein was associated with RNA, and removal of the RNA resulted in a significant reduction in GTPase activity. The RNA associated with GST-Era was shown to be predominantly 16S rRNA. The native Era protein isolated directly from S. pneumoniae was also present as a high-molecular-mass species (600 kDa) complexed with RNA. Together, our results suggest that 16S rRNA is associated with Era and might stimulate its GTPase activity.
PMCID: PMC94028  PMID: 10464193
21.  Genome wide transcriptional profiling in breast cancer cells reveals distinct changes in hormone receptor target genes and chromatin modifying enzymes after proteasome inhibition 
Molecular carcinogenesis  2008;47(11):845-885.
Steroid hormone receptors, like glucocorticoid (GR) and estrogen receptors (ER), are master regulators of genes that control many biological processes implicated in health and disease. Gene expression is dependent on receptor levels which are tightly regulated by the ubiquitin-proteasome system. Previous studies have shown that proteasome inhibition increases GR, but decreases ER-mediated gene expression. At the gene expression level this divergent role of the proteasome in receptor-dependent transcriptional regulation is not well understood. We have used a genomic approach to examine the impact of proteasome activity on GR and ER-mediated gene expression in MCF-7 breast cancer cells treated with dexamethasone (DEX) or 17β-estradiol (E2), the proteasome inhibitor MG132 (MG) or MG132 and either hormone (MD or ME2) for 24h. Transcript profiling reveals that inhibiting proteasome activity modulates gene expression by GR and ER in a similar manner in that several GR and ER target genes are up-regulated and down-regulated after proteasome inhibition. In addition, proteasome inhibition modulates receptor-dependent genes involved in the etiology of a number of human pathological states, including multiple myeloma, leukemia, breast/prostate cancer, HIV/AIDS and neurodegenerative disorders. Importantly, our analysis reveals that a number of transcripts encoding histone and DNA modifying enzymes, prominently histone/DNA methyltransferases and demethylases, are altered after proteasome inhibition. As proteasome inhibitors are currently in clinical trials as therapy for multiple myeloma, HIV/AIDs and leukemia, the possibility that some of the target molecules are hormone regulated and by chromatin modifying enzymes is intriguing in this era of epigenetic therapy.
doi:10.1002/mc.20440
PMCID: PMC2863309  PMID: 18381591
Proteasome inhibitor; receptors: glucocorticoid; estrogen; gene expression profiling; microarray analysis
22.  Perspective beyond Cancer Genomics: Bioenergetics of Cancer Stem Cells 
Yonsei Medical Journal  2010;51(5):617-621.
Although the notion that cancer is a disease caused by genetic and epigenetic alterations is now widely accepted, perhaps more emphasis has been given to the fact that cancer is a genetic disease. It should be noted that in the post-genome sequencing project period of the 21st century, the underlined phenomenon nevertheless could not be discarded towards the complete control of cancer disaster as the whole strategy, and in depth investigation of the factors associated with tumorigenesis is required for achieving it. Otto Warburg has won a Nobel Prize in 1931 for the discovery of tumor bioenergetics, which is now commonly used as the basis of positron emission tomography (PET), a highly sensitive noninvasive technique used in cancer diagnosis. Furthermore, the importance of the cancer stem cell (CSC) hypothesis in therapy-related resistance and metastasis has been recognized during the past 2 decades. Accumulating evidence suggests that tumor bioenergetics plays a critical role in CSC regulation; this finding has opened up a new era of cancer medicine, which goes beyond cancer genomics.
doi:10.3349/ymj.2010.51.5.617
PMCID: PMC2908886  PMID: 20635433
Cancer; genetics; bioenergetics; cancer stem cells
23.  Genome-scale approaches to the epigenetics of common human disease 
Traditionally, the pathology of human disease has been focused on microscopic examination of affected tissues, chemical and biochemical analysis of biopsy samples, other available samples of convenience, such as blood, and noninvasive or invasive imaging of varying complexity, in order to classify disease and illuminate its mechanistic basis. The molecular age has complemented this armamentarium with gene expression arrays and selective analysis of individual genes. However, we are entering a new era of epigenomic profiling, i.e., genome-scale analysis of cell-heritable nonsequence genetic change, such as DNA methylation. The epigenome offers access to stable measurements of cellular state and to biobanked material for large-scale epidemiological studies. Some of these genome-scale technologies are beginning to be applied to create the new field of epigenetic epidemiology.
doi:10.1007/s00428-009-0847-2
PMCID: PMC3107986  PMID: 19844740
Epigenetics; Epidemiology; DNA methylation
24.  Aberrant DNA Methylation Is Associated with Disease Progression, Resistance to Imatinib and Shortened Survival in Chronic Myelogenous Leukemia 
PLoS ONE  2011;6(7):e22110.
The epigenetic impact of DNA methylation in chronic myelogenous leukemia (CML) is not completely understood. To elucidate its role we analyzed 120 patients with CML for methylation of promoter-associated CpG islands of 10 genes. Five genes were identified by DNA methylation screening in the K562 cell line and 3 genes in patients with myeloproliferative neoplasms. The CDKN2B gene was selected for its frequent methylation in myeloid malignancies and ABL1 as the target of BCR-ABL translocation. Thirty patients were imatinib-naïve (mostly treated by interferon-alpha before the imatinib era), 30 were imatinib-responsive, 50 were imatinib-resistant, and 10 were imatinib-intolerant. We quantified DNA methylation by bisulfite pyrosequencing. The average number of methylated genes was 4.5 per patient in the chronic phase, increasing significantly to 6.2 in the accelerated and 6.4 in the blastic phase. Higher numbers of methylated genes were also observed in patients resistant or intolerant to imatinib. These patients also showed almost exclusive methylation of a putative transporter OSCP1. Abnormal methylation of a Src suppressor gene PDLIM4 was associated with shortened survival independently of CML stage and imatinib responsiveness. We conclude that aberrant DNA methylation is associated with CML progression and that DNA methylation could be a marker associated with imatinib resistance. Finally, DNA methylation of PDLIM4 may help identify a subset of CML patients that would benefit from treatment with Src/Abl inhibitors.
doi:10.1371/journal.pone.0022110
PMCID: PMC3132778  PMID: 21760961
25.  Using Protein Domain Microarrays to Read the Histone Code 
For cells to survive, differentiate, and grow, information has to be transferred from the cell surface to the nucleus. This process is referred to as signal transduction. A hallmark of cancer is the deregulation of signal transduction pathways. Signaling events in eukaryotic cells involve the assembly and disassembly of large protein-protein complexes. These diverse associations are mediated through interactions of a limited number of modular signaling units or protein-domains. Protein interactions involving domains are often regulated by posttranslational modification (PTM –like phosphorylation, methylation and acetylation) of the smaller protein motif within the ligand. We have developed a chip-size protein microarray that harbors a display of over 300 modular protein-interacting domains including SH2, SH3, PDZ, FHA, 14-3-3, WW, Chromo, Tudor, PHD and MBT domains. In the emerging proteomic era, it is becoming easier to identify proteins using tryptic digestion followed by mass spectrometric approaches. These same methods also detect sites of posttranslational modification on proteins. Many of these posttranslational modifications likely generate docking sites for protein modules. We have developed protein-domain microarray technology to help identify proteins that can interact with motifs that are either methylated or phosphorylated. This high-throughput approach facilitates the rapid identification of protein-protein interactions in vitro. Further in vivo studies are needed to confirm that these interactions do indeed occur in biological systems. Protein domains are cloned into a GST expression vector, and recombinant protein is produced in bacteria. These fusion proteins are then arrayed onto nitrocellulose coated glass slides using a robot. These slides are probed with biotinylated peptides that are preconjugated to streptavidin-Cy3. The peptides used in this experiment are synthesized as 15 mers, and both the modified and unmodified forms of the peptides are tested on the array. In this manner, we can identify novel methyl- and phospho-dependent interactions. We have built three types of arrays: (1) A phospho-tyrosine reader harbors 70 SH2 domains and 5 PTB domains (total = 75 domains). (2) A phosphothreonine/serine reader that harbors 7 14-3-3 domains, 5 FHA domains, 15 BRCT domains and a WW domain (total = 28 domains). (3) An epigenetic reading array that harbors methyl and acetyl readers. This array is composed of 50 tudor domains, 22 bromo domains, 36 PHD domains, 17 MBT domains, 11 WD40 domains, 9 SANT domains, 28 chromo domains, 15 PWWP domains, 5 BRK domains, 5 CW domains, and 9 Ank repeats (total = 207 domains). More and more posttranslational modifications are being discovered on proteins. The roles of many of these methylation and phosphorylation events often remain obscure. This approach provides an easy way for a researcher to identify potential binding partners for their favorite proteins. These arrays thus offer researchers tools to get at “mechanism”. Once investigators know that they are working with a clearly functional PTM, they can proceed with confidence to generate modification specific antibodies and interrogate the signaling pathway that is engaged by the identified PTM-driven protein-protein interaction.
PMCID: PMC3186674

Results 1-25 (16420)