Genetic Blueprint Research Articles

Influence of 23 coronary artery disease variants on recurrent myocardial infarction or cardiac death: the GRACE Genetics Study

A pooled analysis of 14 genome-wide association studies revealed 23 susceptibility loci for coronary artery disease (CAD), thereby providing the most comprehensive genetic blueprint of CAD susceptibility. Here, we evaluated whether these 23 loci also predispose to recurrent myocardial infarction (MI) or cardiac death following an acute coronary syndrome (ACS). A total of 2099 ACS patients enrolled in the Global Registry of Acute Coronary Events (GRACE) UK-Belgian study were prospectively followed for a median of 5 years (1668 days). C-allele carriers of the rs579459 variant, which is located upstream of the ABO gene and correlates with blood group A, were independently associated with recurrent MI [multivariable-adjusted hazard ratio (HR) 2.25, CI = 1.37-3.71; P = 0.001] and with recurrent MI or cardiac death [multivariable-adjusted (HR) 1.80, CI = 1.09-2.95; P = 0.021] within 5 years after an index ACS. The association of rs579459 was replicated in 1250 Polish patients with 6 months follow-up after an index ACS [multivariable-adjusted (HR) 2.70, CI = 1.26-5.82; P = 0.011 for recurrent MI]. Addition of rs579459 to a prediction model of 17 clinical risk factors improved risk classification for recurrent MI or cardiac death at 6 months as calculated by the integrated discrimination improvement method (P = 0.037), but not by C-statistics (P = 0.096). In this observational study, rs579459 was independently associated with adverse cardiac outcome after ACS. A weak improvement in clinical risk prediction was also observed, suggesting that rs579459 should be further tested as a potentially relevant contributor to risk prediction models for adverse outcome following ACS.

Evolution, Genetic Engineering, and Human Enhancement

There are many ways that biological theory can inform ethical discussions of genetic engineering and biomedical enhancement. In this essay, we highlight some of these potential contributions, and along the way provide a synthetic overview of the papers that comprise this special issue. We begin by comparing and contrasting genetic engineering with programs of selective breeding that led to the domestication of plants and animals, and we consider how genetic engineering differs from other contemporary biotechnologies such as embryo selection. We go on to consider the implications of genetic engineering for human nature, human evolution, and persistence of the human species. Finally, we question whether genetic interventions warrant the extraordinary ethical scrutiny they are often given, and we show how the misleading “genetic blueprint” metaphor has imposed a faulty structure on the enhancement debate. We conclude by considering the nature of biological development and the sobering limits it places on what genetic engineering can reasonably hope to achieve

Chromo Me Thriptic-chaos amongst the chromosomes!

Chromo Me Thriptic-chaos amongst the chromosomes!

A call for an expanded synthesis of developmental and evolutionary paradigms

Charney's target article continues a critique of genetic blueprint models of development that suggests reconsideration of concepts of adaptation, inheritance, and environment, which can be well illustrated in current research on infant attachment. The concepts of development and adaptation are so heavily based on the model of genetics and inheritance forged in the modern synthesis that they will require reconsideration to accommodate epigenetic inheritance.

Bioresearches of Fragile Ecosystem/Desert

The proponents of anthropocene (the era of human-induced climatic changes) suggest that unless humanity changes its behavior according to earth system rules there will be no more holocene-type relative stability. Even the sustainability of the Earth’s life support systems is threatened. Humans and their use of land have transformed more than three quarters of the terrestrial biosphere into anthropogenic biomes. According to Rockstrom and Karlberg, humanity has entered a new phase of sustainability challenges, the Anthropocene, in which human development has reached a scale where it affects vital planetary processes. The earth system is under the pressure from a quadruple squeeze. The human-induced carbon and nitrogen (N) fertilizers are generating a strong imbalance with phosphorous (P). Global fresh water resources are, and will increasingly be, a fundamental limiting factor in feeding the world. By 2025, two third of the world’s population could be living under water-critical conditions. Arid regions (drylands) cover about 45 % of earth’s land surface; they constitute the largest biome on the planet. The dryland forests takes up carbon at rates similar to those of pine forests. In this millennium, global drylands face a myriad of problems that present research, management and policy challenges. Climate change/global warming is great threats to life supporting systems of the desert: drought and heat-induced die-back/drying/deaths and climate-driven vegetation/tree mortality in fragile ecosystems are great concerns. Introduction of alien/invasive species and cultivation of plants with unfavorable water footprint are threat to fragile ecosystems. The study of plant biology in the 21st century is, and will continue to be, vastly different from that in the 20th century. One driver for this has been the use of genomics methods to reveal the genetic blueprints for not one but dozens of plant species. Plant genomics researchers have readily embraced new algorithms, technologies and approaches to generate genome, transcriptome and epigenome datasets for model and crop species that have permitted deep inferences into plant biology. At the Department of Botany, Jai Narain Vyas University, Jodhpur; with the help of Department of Biotechnology, Department of Science and Technology, Government of India and the University Grants Commission of India, we have developed biotechnological methods for characterization, conservation, propagation and improvement of plants of Rajasthan. These are described and discussed in this paper. A few recommendations, useful for the desert ecosystem and bio-resources are submitted.

Translating genomic information into clinical medicine: lung cancer as a paradigm.

We are currently in an era of rapidly expanding knowledge about the genetic landscape and architectural blueprints of various cancers. These discoveries have led to a new taxonomy of malignant diseases based upon clinically relevant molecular alterations in addition to histology or tissue of origin. The new molecularly based classification holds the promise of rational rather than empiric approaches for the treatment of cancer patients. However, the accelerated pace of discovery and the expanding number of targeted anti-cancer therapies present a significant challenge for healthcare practitioners to remain informed and up-to-date on how to apply cutting-edge discoveries into daily clinical practice. In this Perspective, we use lung cancer as a paradigm to discuss challenges related to translating genomic information into the clinic, and we present one approach we took at Vanderbilt-Ingram Cancer Center to address these challenges.

Emerging roles for the pro-oncogenic anterior gradient-2 in cancer development

Clinical studies have defined the core 'genetic blueprint' of a cancer cell, but this information does not necessarily predict the cancer phenotype. Signalling hubs that mediate such phenotype have been identified largely using OMICS platforms that measure dynamic molecular changes within the cancer cell landscape. The pro-oncogenic protein anterior gradient 2 (AGR2) is a case in point; AGR2 has been shown using a range of expression platforms to be involved in asthma, inflammatory bowel disease, cell transformation, cancer drug resistance and metastatic growth. AGR2 protein is also highly overexpressed in a diverse range of human cancers and can be secreted and detected in extracellular fluids, thus representing a compelling pro-oncogenic signalling intermediate in human cancer. AGR2 belongs to the protein disulphide isomerase family with all the key features of an endoplasmic reticulum-resident protein-this gives clues into how it might function as an oncoprotein through the regulation of protein folding, maturation and secretion that can drive metastatic cell growth. In this review, we will describe the known aspects of AGR2 molecular biology, including gene structure and regulation, emerging protein interaction networks and how its subcellular localization mediates its biological functions. We will finally review the cases of AGR2 expression in human cancers, the pathophysiological consequences of AGR2 overexpression, its potential role as a tumour biomarker that predicts the response to therapy and how the AGR2 pathway might form the basis for drug discovery programmes aimed at targeting protein folding/maturation pathways that mediate secretion and metastasis.

Genes & cells: Sperm's genetic blueprint compiled: Analysis uses sex cells to calculate human mutation rates

Genes & cells: Sperm's genetic blueprint compiled: Analysis uses sex cells to calculate human mutation rates

Fundamental concepts of epigenetics for consideration in anesthesiology

Epigenetics dictate how the genetic blueprint is ultimately expressed and, therefore, is fundamental to our understanding of disease etiology and cellular responses and consequences to exposure of stimuli, such as anesthetics and perioperative stress. The goal of this review is to provide a concise overview of the fundamental concepts in epigenetics and discuss how epigenetics may be incorporated into research studies in anesthesiology. Chemical modifications of DNA and core histone proteins are epigenetic marks that constitute the functional genome and are key to generating diverse cellular phenotypes from the same genotype. These modifications and the cellular machineries that regulate them are essential for maintaining tissue-specific and timing-specific expression profiles for normal functioning and can be altered in disease contexts, thus providing the molecular basis for the abnormalities. Similar to determining cellular identity within a person, epigenetic differences between individuals, including monozygotic twins, can account for disparate phenotypes in the absence of genetic variation in the genes of interest. Furthermore, epigenetic modifications are dynamic but heritable and, thus, are fitting for reinforcing adaptive phenotypes in response to external stimuli. Epigenetic mechanisms underlie many human pathological conditions and impact clinical management in a variety of contexts. Although epigenetic research related to anesthesiology is sparse at the present, the full understanding of the mechanism of action of analgesics, interindividual variations in responses to anesthetics and consequences of exposure to anesthetic drugs will likely require the evaluation and integration of epigenetic information into current research paradigms.

Sequencing Intractable DNA to Close Microbial Genomes

Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled “intractable” resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the “non-contiguous finished” Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

Ciliated protozoa are peculiar for their nuclear dimorphism, wherein two types of nuclei divide nuclear functions: a germline micronucleus (MIC) is transcriptionally inert during vegetative growth, but serves as the genetic blueprint for the somatic macronucleus (MAC), which is responsible for all transcripts supporting cell growth and reproduction. While all the advantages/disadvantages associated with nuclear dimorphism are not clear, an essential advantage seems to be the ability to produce a highly polyploid MAC, which then allows for the maintenance of extremely large single cells — many ciliate cells are larger than small metazoa. In some ciliate classes, chromosomes in the MAC are extensively fragmented to create extremely short chromosomes that often carry single genes, and these chromosomes may be present in different copy numbers, resulting in different ploidies. While using gene copy number to regulate gene expression is limited in most eukaryotic systems, the extensive fragmentation in some ciliate classes provides this opportunity to every MAC gene. However, it is still unclear if this mechanism is in fact used extensively in these ciliates. To address this, we have quantified copy numbers of 11 MAC chromosomes and their gene expression in Oxytricha trifallax (CI: Spirotrichea). We compared copy numbers between two subpopulations of O. trifallax, and copy numbers of 7 orthologous genes between O. trifallax and the closely related Stylonychia lemnae. We show that copy numbers of MAC chromosomes are variable, dynamic, and positively correlated to gene expression. These features might be conserved in all spirotrichs, and might exist in other classes of ciliates with heavily fragmented MAC chromosomes.

Hippocampal mGluR5 predicts an occurrence of helplessness behavior after repetitive exposure to uncontrollable stress

An individual's behavior is generally based on genetic blueprint and previous experiences. A coping strategy, affected by personal interpretation of past events, can be determined by behavioral controllability of stress. In this study, we examined the relationship between the hippocampal mGluR5 expression and coping strategies to stress. Rats were exposed to stress via inescapable and unpredictable footshocks on PNDs 14 and 90. Coping strategies to stress were also measured. Hippocampal mGluR5 was found to be linked to the behavioral coping strategy, as it increased in rats that showed helplessness behavior (HL (+) group) and decreased in those that did not (HL (−) group). Also, the HL (+) group showed a lack of adaptation in a novel environment but the HL (−) group did not. The results suggest that mGluR5 has a pivotal role in the controllability-based coping strategy. Hippocampal mGluR5 could be a target molecule in the manipulation of neuropsychiatric conditions for which maladaptation is a part of behavioral consequences.

Genes & cells: DNA flunks disease predicting test: Genetic blueprint can foretell risk for only a few disorders

Genes & cells: DNA flunks disease predicting test: Genetic blueprint can foretell risk for only a few disorders

Abstract SY25-03: Host and tumor genetic architecture influence clinically relevant oncogenic pathways in neuroblastoma

Abstract Cancer research is at a critical crossroads as genomic technologies have enabled potentially paradigm-shifting discoveries in host genetic alterations that lead to cancer, as well as the major oncogenic drivers that somatically arise and shape the ultimate tumor phenotype. Approaches such as genome-wide association studies (GWAS) to discover heritable susceptibility variants have largely occurred in parallel with tumor profiling efforts designed to discover somatically acquired mutations. We see tremendous opportunity in integrating these efforts under the broad hypothesis that the host's genetic blueprint not only influences susceptibility to cancer, but also significantly influences the cancer phenotype at diagnosis and the pathways upon which the cancer is dependent. By focusing our efforts on the pediatric cancer neuroblastoma, we are directly addressing an important childhood malignancy that continues to exact disproportionate morbidity and mortality. However, we have also shown that this disease also serves as a remarkable model for the study of human cancers in general, and we think that lessons learned here are likely to be more broadly applicable as we are addressing the concept that somatic mutations alone will not define the entire spectrum of oncogenic vulnerabilities in cancer cells. Until recently, the etiology of neuroblastoma was unknown. By studying the 1% of neuroblastoma cases that occur within families, we have discovered ALK and PHOX2B as the two major hereditary predisposition genes.1,2 In parallel, by studying the 99% of cases that occur sporadically in our ongoing GWAS, for which we have now analyzed 4,000 cases and 10,000 controls, we have shown that normal genetic variation at multiple loci influences neuroblastoma susceptibility.3-7 We have several other recently validated associations that are not yet published, including replicated signals in LIN28B and HACE1. Significant lessons from the GWAS to date include: 1) Neuroblastoma is a genetic disease; 2) every signal identified to date is intragenic; 3) associations are enriched in phenotypic subsets; and 4) many of the genes identified by the neuroblastoma GWAS not only influence malignant transformation of a developing neuroblastic cell, but also contribute to the maintenance of the malignant phenotype. For example, SNP variations in the LMO1 gene are highly associated with overexpression of this transcriptional co-factor, and genetic manipulation of expression shows that it functions as an oncogenic driver in a genotype specific manner.7 In other words, our data suggest that subjects harboring LMO1 risk alleles are much more likely to have tumors dependent on LMO1-influenced transcriptional regulation suggesting that oncogene addiction is also hardwired in the heritable genome. In parallel, we and others have shown that somatic activating mutations in the ALK kinase domain occur in ∼10% of sporadic cases.2,8-10 To seek other potential somatically acquired mutations that may be therapeutically relevant in the neuroblastoma coding genome, we have resequenced 99 high-risk neuroblastoma cases using a combination of whole exome, genome and transcriptome sequencing. Tumors contained a median 0.56 non-silent mutations per megabase of coding DNA, one of the lowest rates reported in cancer to date. ALK was the most commonly mutated gene (9%), and no other gene showed mutation frequency rates >5%. These data clearly indicate that somatic mutation in neuroblastoma is relatively rare, leading to the concept that other mechanisms, such as host polymorphic variation or germline mutations in key regulatory regions, play an important role in tumorigenesis. Ongoing work to be discussed at the symposium include efforts to identify and validate rare variants in the host genome that impact neuroblastoma susceptibility, understanding the functional relevance of DNA variation in the developing neuroblastoma and in tumor tissues, completion of our cataloguing of somatic mutations in high-risk disease, and efforts to understand the impact of non-coding DNA alterations in the host in tumor genomes on neuroblastoma clinical phenotype. Efforts to translate these efforts into deliverables for the clinic will be emphasized.

Structure modeling and mutational analysis of gap junction beta 2 (GJB2)

The genome sequencing accomplishes complete genetic blue prints for hundreds of organisms, including humans. In the current era, we are trying to focus on analyzing, controlling and modifying functions of proteins encoded by these genomes. This task is attained by protein three dimensional structures. Three dimensional (3 D) structure is very useful for understanding biological functions. Gap junction beta 2 (GJB2), human gene encoding for gap junction beta 2 protein is involved in various hearing disorders in Pakistani families. After the first report of GJB2 involvement in Pakistani families, it was necessary to further study this protein. Therefore, a 3D structure of GJB2 was developed using comparative modeling approach. For modeling, a template was selected by blastp at NCBI and the best template selected was 2ZW3. By comparing the template-target sequence, a model was created using MODELLER, a program for homology modeling. The accuracy of the predicted structure was checked using Ramachandran plot which showed that the residue falling in the favored region was 92.4%. The predicted GJB2 model can be used to understand the defects that lead to deafness and eventually in drug designing. Domains and different properties of GJB2 were analyzed by applying online servers. Most frequent mutations of GJB2 were discussed by differentiating between damaging and benignity. Key words : GJB2, 3D structure, 2ZW3, DFNB1, MODELLER.

Advances in plant genome sequencing

The study of plant biology in the 21st century is, and will continue to be, vastly different from that in the 20th century. One driver for this has been the use of genomics methods to reveal the genetic blueprints for not one but dozens of plant species, as well as resolving genome differences in thousands of individuals at the population level. Genomics technology has advanced substantially since publication of the first plant genome sequence, that of Arabidopsis thaliana, in 2000. Plant genomics researchers have readily embraced new algorithms, technologies and approaches to generate genome, transcriptome and epigenome datasets for model and crop species that have permitted deep inferences into plant biology. Challenges in sequencing any genome include ploidy, heterozygosity and paralogy, all which are amplified in plant genomes compared to animal genomes due to the large genome sizes, high repetitive sequence content, and rampant whole- or segmental genome duplication. The ability to generate de novo transcriptome assemblies provides an alternative approach to bypass these complex genomes and access the gene space of these recalcitrant species. The field of genomics is driven by technological improvements in sequencing platforms; however, software and algorithm development has lagged behind reductions in sequencing costs, improved throughput, and quality improvements. It is anticipated that sequencing platforms will continue to improve the length and quality of output, and that the complementary algorithms and bioinformatic software needed to handle large, repetitive genomes will improve. The future is bright for an exponential improvement in our understanding of plant biology.

Development of fetal trabecular micro‐architecture in the humerus and femur

It is widely accepted that during postnatal development trabecular bone adapts to the prevailing loading environment via modelling. However, very little is known about the mechanisms (whether it is predominantly modelling or remodelling) or controls (such as whether loading influences development) of fetal bone growth. In order to make inferences about these factors, we assessed the pattern of fetal trabecular development in the humerus and femur via histomorphometric parameter quantification. Growth and development (between 4 and 9 months prenatal) of trabecular architecture (i.e. thickness, number and bone volume fraction) was compared across upper and lower limb bones, proximal and distal regions, and sexes. The data presented here indicate that during prenatal development trabeculae became thicker and less numerous, whilst bone volume fraction remained constant. This partly mimics the pattern of early postnatal development (0-2 years) described by other researchers. Thickness was reported to increase whilst number reduced, but bone volume fraction decreased. This is perhaps because the balance of bone modelling (deposition vs. resorption) changes post partum. Published histological data suggest that bone deposition slows after birth, while resorption rates remain constant. Hence, fetal development may be characterized by relatively high rates of modelling and, particularly, bone deposition in comparison to postnatal. With respect to measures of thickness, number and bone volume fraction prenatal development was not bone, site, or sex specific, whilst postnatally these measures of architecture diverge. This is despite reported developmental variation in the frequency, speed and amplitude of fetal movements (which begin after 11 weeks and continue until birth), and probably therefore loading induced by muscular contractions. This may be because prenatal limb bone micro-architecture follows a generalised predetermined growth trajectory (or genetic blueprint), as appears to be the case for gross distribution of trabecular tissue.

Bringing trees into the fuel line

Bringing trees into the fuel line

Guest commentary: The human microbiome and the promise of clinical ecology

Metagenomics, the application of high-throughput sequencing to nucleic acids extracted directly from environmental samples, made its debut in 2004 through two high-profile papers in Science (Sargasso Sea) and Nature (acid mine drainage). A key strength of the approach is the ability to circumvent the well-known cultivation bottleneck and lay bare the genetic blueprints of ecologically important members of the microbial community, many of which cannot be easily obtained in culture.

Multi-Cellular Logistics of Collective Cell Migration

During development, the formation of biological networks (such as organs and neuronal networks) is controlled by multicellular transportation phenomena based on cell migration. In multi-cellular systems, cellular locomotion is restricted by physical interactions with other cells in a crowded space, similar to passengers pushing others out of their way on a packed train. The motion of individual cells is intrinsically stochastic and may be viewed as a type of random walk. However, this walk takes place in a noisy environment because the cell interacts with its randomly moving neighbors. Despite this randomness and complexity, development is highly orchestrated and precisely regulated, following genetic (and even epigenetic) blueprints. Although individual cell migration has long been studied, the manner in which stochasticity affects multi-cellular transportation within the precisely controlled process of development remains largely unknown. To explore the general principles underlying multicellular migration, we focus on the migration of neural crest cells, which migrate collectively and form streams. We introduce a mechanical model of multi-cellular migration. Simulations based on the model show that the migration mode depends on the relative strengths of the noise from migratory and non-migratory cells. Strong noise from migratory cells and weak noise from surrounding cells causes “collective migration,” whereas strong noise from non-migratory cells causes “dispersive migration.” Moreover, our theoretical analyses reveal that migratory cells attract each other over long distances, even without direct mechanical contacts. This effective interaction depends on the stochasticity of the migratory and non-migratory cells. On the basis of these findings, we propose that stochastic behavior at the single-cell level works effectively and precisely to achieve collective migration in multi-cellular systems.