New cancer treatment gives hope to lymphoma and leukemia patients (TGen)

Cancer researchers have high hopes for a new therapy for patients with certain types of lymphoma and leukemia. PCI-32765 is a new drug being assessed in a Phase I clinical trial at the Virginia G. Piper Cancer Center in collaboration with the Clinical Division of the Translational Genomics Research Institute (TGen). This is one of 35 such trials under way through a partnership between the Virginia G. Piper Cancer Center at Scottsdale Healthcare and TGen, which enables molecular and genomic discoveries to reach patients through Phase I trials as quickly as possible.

“Progress in developing new treatments for cancer has been painfully slow as only 2-4 percent of all cancer patients enroll in clinical trials. This is especially true for uncommon cancers such as leukemia’s and lymphomas,” said Dr. Raoul Tibes, Director of the Hematological Malignancies Program at the Virginia G. Piper Cancer Center and an Associate Investigator at TGen.

Clinical trials test the safety and effectiveness of new drugs prior to approval by the U.S. Food and Drug Administration. Participants are volunteers for whom other cancer treatments have failed. Arizona is one of many states in which clinical trials often are covered by health insurance. “This study is going very well. It is a very promising agent,’’ Dr. Tibes said of PCI-32765, which uniquely targets the molecular abnormalities of lymphoma cells. “This is a recently identified cancer mechanism that we are going after with this drug in lymphoma cells.” Visit the TGen portal for complete study findings

Computational Complementation (PLoS)

Autoregulation of nodulation (AON) is a long-distance, shoot-root signalling system for regulating nodule formation in legume plants. This visualisation, taken from a computational complementation experiment, demonstrates the possible allocation of an unidentified signal for inhibition of nodulation in soybean root. In this approach, an empirical model of a loss-of-function (non-AON) mutant is complemented with hypothetical AON mechanisms. If the resulting nodulation phenotype matches the wild-type plant, the hypotheses would be supported as reasonable. The first application of computational complementation predicted that soybean cotyledons participate in AON, which was subsequently confirmed by a real-plant experiment (see Han et al., doi:10.1371/journal.pcbi.1000685). Visit the PLoS portal for comeplte study findings

Genome-wide analysis of histone modifications in human pancreatic islets

The global diabetes epidemic poses a major challenge. Epigenetic events contribute to the etiology of diabetes; however, the lack of epigenomic analysis has limited the elucidation of the mechanistic basis for this link. To determine the epigenetic architecture of human pancreatic islets we mapped the genome-wide locations of four histone marks: three associated with gene activation—H3K4me1, H3K4me2, and H3K4me3—and one associated with gene repression, H3K27me3. Interestingly, the promoters of the highly transcribed insulin and glucagon genes are occupied only sparsely by H3K4me2 and H3K4me3.

Globally, we identified important relationships between promoter structure, histone modification, and gene expression. We demonstrated co-occurrences of histone modifications including bivalent marks in mature islets. Furthermore, we found a set of promoters that is differentially modified between islets and other cell types. We also use our histone marks to determine which of the known diabetes-associated single-nucleotide polymorphisms are likely to be part of regulatory elements. Our global map of histone marks will serve as an important resource for understanding the epigenetic basis of type 2 diabetes. The Genome Research portal provides complete study findings

Benefits of Osiris’ Mesenchymal Stem Cell Therapy Confirmed in Late-Stage Studies against SR-GvHD

Osiris Therapeutics’ stem cell product Prochymal showed significant benefits as a treatment for steroid-refractory acute graft vs. host disease (SR-GvHD) in both adults and children, according to Phase III trial results. Prochymal comprises a preparation of expanded mesenchymal stem cells (MSC) derived from the bone marrow of healthy young adult donors. The stem cells are formulated for intravenous administration. Data from a Phase III trial (Protocol 280) in adults are being presented at the 2010 BMT Tandem Meeting. The study included 244 patients with GvHD, who were treated using either Prochymal or placebo in addition to standard-of-care therapy.

Overall results showed that the addition of Prochymal resulted in a 76% response rate among patients with steroid-refractory liver and an 82% response rate for patients with gastrointestinal GvHD. For individuals with GvHD affecting the skin, liver, and gastrointestinal tract, treatment with Prochymal produced a 63% overall response rate. None of the placebo-treated patients in this group responded.

The pediatric trial (Protocol 275) showed that Prochymal therapy resulted in a 64% overall response rate compared with 36% for the placebo group. Treatment with Prochymal also more than doubled the complete response rate to 64% and halved disease progression to 21%. The GEN portal provies complete research findings

Integrative analysis of the melanoma transcriptome (Genome Research)

Global studies of transcript structure and abundance in cancer cells enable the systematic discovery of aberrations that contribute to carcinogenesis, including gene fusions, alternative splice isoforms, and somatic mutations. We developed a systematic approach to characterize the spectrum of cancer-associated mRNA alterations through integration of transcriptomic and structural genomic data, and we applied this approach to generate new insights into melanoma biology.

Using paired-end massively parallel sequencing of cDNA (RNA-seq) together with analyses of high-resolution chromosomal copy number data, we identified 11 novel melanoma gene fusions produced by underlying genomic rearrangements, as well as 12 novel readthrough transcripts. We mapped these chimeric transcripts to base-pair resolution and traced them to their genomic origins using matched chromosomal copy number information. We also used these data to discover and validate base-pair mutations that accumulated in these melanomas, revealing a surprisingly high rate of somatic mutation and lending support to the notion that point mutations constitute the major driver of melanoma progression. Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types. Visit the Genome Research portal for complete study findings

A Multi-Strategy Approach to Informative Gene Identification from Gene Expression Data (JBCB)

An unsupervised multi-strategy approach has been developed to identify informative genes from high throughput genomic data. Several statistical methods have been used in the field to identify differentially expressed genes. Since different methods generate different lists of genes, it is very challenging to determine the most reliable gene list and the appropriate method. This paper presents a multi-strategy method, in which a combination of several data analysis techniques are applied to a given dataset and a confidence measure is established to select genes from the gene lists generated by these techniques to form the core of our final selection.

The remainder of the genes that form the peripheral region are subject to exclusion or inclusion into the final selection. This paper demonstrates this methodology through its application to an in-house cancer genomics dataset and a public dataset. The results indicate that our method provides more reliable list of genes, which are validated using biological knowledge, biological experiments, and literature search. We further evaluated our multi-strategy method by consolidating two pairs of independent datasets, each pair is for the same disease, but generated by different labs using different platforms. The results showed that our method has produced far better results. The JBCB web site the complete research findings

Examination of transcriptional networks reveals an important role for TCFAP2C, SMARCA4, and EOMES in trophoblast stem cell maintenance

Trophoblast stem cells (TS cells), derived from the trophectoderm (TE) of blastocysts, require transcription factors (TFs) and external signals (FGF4, INHBA/NODAL/TGFB1) for self-renewal. While many reports have focused on TF networks that regulate embryonic stem cell (ES cell) self-renewal and pluripotency, little is know about TF networks that regulate self-renewal in TS cells. To further understand transcriptional networks in TS cells we used chromatin immunopreciptiation and DNA microarray analysis (ChIP-chip) to investigate targets of TFs TCFAP2C, EOMES, ETS2, and GATA3, and a chromatin remodeling factor, SMARCA4. We then evaluated the transcriptional states of target genes using transcriptome analysis and genome-wide analysis of histone H3 acetylation (AcH3). Our results describe previously unknown transcriptional networks in TS cells, including TF occupancy of genes involved in ES cell self-renewal and pluripotency, co-occupancy of TCFAP2C, SMARCA4, and EOMES at a significant number of genes, and transcriptional regulatory circuitry within the 5 factors.

Moreover, RNAi depletion of Tcfap2c, Smarca4, and Eomes transcripts resulted in a loss of normal colony morphology and downregulation of TS cell specific genes, suggesting an important role for TCFAP2C, SMARCA4, and EOMES in TS cell self-renewal. Through genome-wide mapping and global expression analysis of 5 TF target genes, our data provide a comprehensive analysis of transcriptional networks that regulate TS cell self-renewal. Visit the Genome Research portal to review the full abstract or order this article

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We optimized bisulfite sequencing for genome-scale analysis of clinical samples: here we outline how restriction digestion targets bisulfite sequencing to hotspots of epigenetic regulation and describe a statistical method for assessing significance of altered DNA methylation patterns. Thirty nanograms of DNA was sufficient for genome-scale analysis and our protocol worked well on formalin-fixed, paraffin-embedded samples. Visit the Nature Methods press portal for full research details

Genomic features defining exonic variants that modulate splicing (Genome Biology)

Single point mutations at both synonymous and non-synonymous positions within exons can have severe effects on gene function through disruption of splicing. Predicting these mutations in-silico purely from the genomic sequence is difficult due to an incomplete understanding of the multiple factors that may be responsible. In addition, little is known about which computational prediction approaches, such as those involving exonic splicing enhancers and exonic splicing silencers, are most informative.

Assessed the features of single-nucleotide genomic variants verified to cause exon-skipping and compared them to a large set of coding SNPs common in the human population, which are likely to have no effect on splicing. Our findings implicate a number of features important for their ability to discriminate splice-affecting variants including the naturally occurring density of exonic splicing enhancers and exonic splicing silencers of the exon and intronic environment, creation of extensive changes in the number of predicted exonic splicing enhancers and exonic splicing silencers, proximity to the splice junctions and evolutionary constraint of the region surrounding the variant. By extending this approach to additional datasets, we also identified relevant features of variants that cause increased exon inclusion and ectopic splice site activation.

Identified a number of features that have statistically significant representation among exonic variants that modulate splicing. These analyses highlight putative mechanisms responsible for splicing outcome and emphasize the role of features important for exon definition. We developed a web-tool, Skippy, to score coding variants for these relevant splice-modulating features.

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes (PLoS Genetics)

The natural transfer of DNA from mitochondria to the nucleus generates nuclear copies of mitochondrial DNA (numts) and is an ongoing evolutionary process, as genome sequences attest. In humans, five different numts cause genetic disease and a dozen human loci are polymorphic for the presence of numts, underscoring the rapid rate at which mitochondrial sequences reach the nucleus over evolutionary time.

In the laboratory and in nature, numts enter the nuclear DNA via non-homolgous end joining (NHEJ) at double-strand breaks (DSBs). The frequency of numt insertions among 85 sequenced eukaryotic genomes reveal that numt content is strongly correlated with genome size, suggesting that the numt insertion rate might be limited by DSB frequency. Polymorphic numts in humans link maternally inherited mitochondrial genotypes to nuclear DNA haplotypes during the past, offering new opportunities to associate nuclear markers with mitochondrial markers back in time. Visit the PLoS Genetics portal for full research details

Amplification of Asynchronous Inhibition-Mediated Synchronization by Feedback in Recurrent Networks (PLoS)

Synchronization of 30–80 Hz oscillatory activity of the principle neurons in the olfactory bulb (mitral cells) is believed to be important for odor discrimination. Previous theoretical studies of these fast rhythms in other brain areas have proposed that principle neuron synchrony can be mediated by short-latency, rapidly decaying inhibition. This phasic inhibition provides a narrow time window for the principle neurons to fire, thus promoting synchrony. However, in the olfactory bulb, the inhibitory granule cells produce long lasting, small amplitude, asynchronous and aperiodic inhibitory input and thus the narrow time window that is required to synchronize spiking does not exist. Instead, it has been suggested that correlated output of the granule cells could serve to synchronize uncoupled mitral cells through a mechanism called “stochastic synchronization”, wherein the synchronization arises through correlation of inputs to two neural oscillators.

Almost all work on synchrony due to correlations presumes that the correlation is imposed and fixed. Building on theory and experiments that we and others have developed, we show that increased synchrony in the mitral cells could produce an increase in granule cell activity for those granule cells that share a synchronous group of mitral cells. Common granule cell input increases the input correlation to the mitral cells and hence their synchrony by providing a positive feedback loop in correlation. Thus we demonstrate the emergence and temporal evolution of input correlation in recurrent networks with feedback. We explore several theoretical models of this idea, ranging from spiking models to an analytically tractable model. The PLoS portal offers complete study findings

Microsonic Systems HENDRIX SM100 Now Serving Solubilization, Thawing, Mixing & Suspension

The HENDRIX SM100 has been enhanced to cover a wider range of applications and to satisfy market demands for higher throughput in sample preparation and fluid processing. Combining the Company’s proprietary lateral ultrasonic thrust™ (LUT) technology and the unique design of the FASA array, the HENDRIX SM100 enables rapid compound solubilization which reduces the hours-long process to minutes. The HENDRIX SM100 can also thaw frozen samples in a matter of minutes; this new use of ultrasonic technology will facilitate the possibility of on-demand sample retrieval. The HENDRIX SM100 can also suspend magnetic particles as well as live cells, which further expands its applications in Life Science to activities such as DNA extraction or isolation.

Microsonic Systems presented a poster at the Lab Automation conference entitled “Mixing Effectiveness – A Methodology and Study of Microplate Mixing Techniques Including Ultrasonic HENDRIX SM100” concluded that the ultrasonic fluid processor is able to mix DMSO samples into water 7 times faster than samples mixed by orbital shaker and 12 times faster than samples mixed by diffusion. The HENDRIX SM100 can cause rapid and effective mixing in just a few minutes, particularly for smaller assay volumes where traditional mixing is hampered by surface tension effects.

Since HENDRIX SM100’s debut in January, 2009, Microsonic Systems has made several product improvements to support a wide range of common labware – 96, 384 and 1536-well plates; flat bottom, U-bottom, V-bottom labware; and 2D-barcoded tubes. Software improvements now allow users to control the system in three distinct ways: through the system’s front touch panel; with a graphical user interface; or by using an API that supports integrated environments. Microsonic Systems intends to extend its applications to other areas in need of high-throughput, parallel ultrasonic fluid processing. The Microsonic Systems product portal offers complete specification and performance details

Genome sequencing of 3 parasitoid wasp species (UAB)

An international consortium of scientists, including Universitat Autònoma de Barcelona (UAB) researcher Deodoro Oliveira, have sequenced the genome of three species of parasitoid wasps of the genus Nasonia. The research offers new basic information on the genetic mechanisms of evolution. It is also of great importance for the control of agricultural pests and of insect-borne diseases, since parasitoid wasps bite and lay eggs on much larger insects, many of which are the ones to later cause plagues or spread infectious diseases. The research could pave the way for new methods of controlling these plagues and preventing the propagation of diseases.

Parasitoid wasps are four times smaller than the common fruit fly. They lay eggs within other insects and kill their host before leaving. Although their size is insignificant, their importance in the control of populations of agricultural pests is crucial. Thanks to these insects billions of euros worth of crops are saved each year. Not only that, but the genus Nasonia is very useful for research carried out in genetics, given that the males evolve from non-fertilised eggs and only have one set of chromosomes, and it is therefore immediately possible to detect the effects of chromosomes which have undergone mutations. In experiments in which mutations take place, the altered genes are easily detected because there is no copy of the gene which could mask the effects.

The research, recently published in the journal Science, shows the full genome sequencing of the species Nasonia vitripennis, Nasonia giraulti and Nasonia longicornis. It also points out key discoveries made with these sequencings, such as the identification of the genes responsible for the venom produced by wasps. Scientists have identified 79 different proteins in this venom, 23 of which had never been observed before. This information could be very useful in the development of new drugs, since these proteins have important physiological effects on the cells of their hosts. With the complete sequencing of these genomes, research also can identify the genes that determine which specific insects will be attacked by the parasitoid wasp, as well as the specific food needs of its offspring at large scale. Visit the UAB press portal for complete study findings

Patterns of cancer’s altered landscape emerge (Broad Institute)

The genome of a cancer cell makes for a bizarre landscape. Compared to the genome of a normal human cell, the cancer genome is distorted - sometimes sections are missing, repeated, or scrambled. Parts of chromosomes may be rearranged so that pieces from one chromosome become attached to another. Some of these mutations are most likely causing, or driving, cancer and could inform drug treatment options for patients. But other mutations are simply along for the ride and have little relevance to cancer's progression or treatment.

To determine which mutations may underlie cancer, researchers want to discern what alterations repeatedly crop up in tumors from different patients. Most likely, these prevalent mutations are not due to random chance: they are the result of cancer cells selecting for mutations that give them the power to grow unchecked and invade surrounding tissue.

To find these alterations, researchers led by Matthew Meyerson, a professor of pathology at the Dana-Farber Cancer Institute and senior associate member at the Broad Institute, amassed data from over 3000 cancer specimens representing more than 26 cancer types. With this much data in hand, researchers from the Broad Institute and the Dana Farber Cancer Institute began to pick out patterns of alterations. So much raw information makes it impractical to see these patterns emerge with the naked eye, so the researchers designed computer algorithms to make important mutations stand out. Their results appear in the February 18 issue of Nature.

Most Recent Common Ancestor of the 17q21 Inversion in Humans (AJHG)

The polymorphic inversion on 17q21, sometimes called the microtubular associated protein tau (MAPT) inversion, is an 900 kb inversion found primarily in Europeans and Southwest Asians. We have identified 21 SNPs that act as markers of the inverted, i.e., H2, haplotype. The inversion is found at the highest frequencies in Southwest Asia and Southern Europe (frequencies of 30%); elsewhere in Europe , frequencies vary from < 5%, in Finns, to 28%, in Orcadians.

Molecular evolution analyses indicate that the H2 haplotype originally arose in Africa or Southwest Asia. Though the H2 inversion has many fixed differences across the 900 kb, short tandem repeat polymorphism data indicate a very recent date for the most recent common ancestor, with dates ranging from 13,600 to 108,400 years, depending on assumptions and estimation methods. This estimate range is much more recent than the 3 million year age estimated by Stefansson et al. in 2005. Visit the american Journal of Human Genetics for complete study findings

Proteomics Analysis of A33 Immunoaffinity-purified Exosomes (Molecular & Cellular Proteomics)

Exosomes are 40–100-nm-diameter nanovesicles of endocytic origin that are released from diverse cell types. To better understand the biological role of exosomes and to avoid confounding data arising from proteinaceous contaminants, it is important to work with highly purified material. Here, we describe an immunoaffinity capture method using the colon epithelial cell-specific A33 antibody to purify colorectal cancer cell (LIM1215)-derived exosomes. LC-MS/MS revealed 394 unique exosomal proteins of which 112 proteins (28%) contained signal peptides and a significant enrichment of proteins containing coiled coil, RAS, and MIRO domains.

A comparative protein profiling analysis of LIM1215-, murine mast cell-, and human urine-derived exosomes revealed a subset of proteins common to all exosomes such as endosomal sorting complex required for transport (ESCRT) proteins, tetraspanins, signaling, trafficking, and cytoskeletal proteins. A conspicuous finding of this comparative analysis was the presence of host cell-specific (LIM1215 exosome) proteins such as A33, cadherin-17, carcinoembryonic antigen, epithelial cell surface antigen (EpCAM), proliferating cell nuclear antigen, epidermal growth factor receptor, mucin 13, misshapen-like kinase 1, keratin 18, mitogen-activated protein kinase 4, claudins (1, 3, and 7), centrosomal protein 55 kDa, and ephrin-B1 and -B2. Furthermore, we report the presence of the enzyme phospholipid scramblase implicated in transbilayer lipid distribution membrane remodeling. The LIM1215-specific exosomal proteins identified in this study may provide insights into colon cancer biology and potential diagnostic biomarkers. For complete details visit the Molecular and Cellular Proteomics portal

A new spin on energy independence (Broad Institute)

In a paper appearing in the February 14 advance online issue of the journal Nature Biotechnology, a team of scientists reports the discovery of a well-known compound that seems to do just that. Their findings could someday spur new ways of preventing or treating a variety of illnesses, including stroke, heart attack and maybe even cancer.
Unlike people, most cells are remarkably flexible in the ways they use, or metabolize, energy, and can readily shift from one method to another depending on the circumstances. For example, cells can switch back and forth from glycolysis, a form of metabolism that relies on the sugar glucose, to another type of metabolism known as mitochondrial respiration, which is more efficient, occurs inside special compartments called mitochondria, and requires the presence of oxygen.
Beyond just a simple observation, this flexibility has garnered attention for its potential utility in treating human disease. For instance, researchers have known for decades that in cancer, cells show a strong preference for glycolysis over other forms of metabolism, and that the way glycolysis proceeds is distinct from normal human cells. Some recent studies suggest that thwarting this cancer cell tendency (known as the "Warburg effect") might help slow tumor growth. Review the complete article via Nature Biotechnology or the Broad Institute portals

A Kinetic Model of Dopamine- and Calcium-Dependent Striatal Synaptic Plasticity

Corticostriatal synapse plasticity of medium spiny neurons is regulated by glutamate input from the cortex and dopamine input from the substantia nigra. While cortical stimulation alone results in long-term depression (LTD), the combination with dopamine switches LTD to long-term potentiation (LTP), which is known as dopamine-dependent plasticity. LTP is also induced by cortical stimulation in magnesium-free solution, which leads to massive calcium influx through NMDA-type receptors and is regarded as calcium-dependent plasticity. Signaling cascades in the corticostriatal spines are currently under investigation. However, because of the existence of multiple excitatory and inhibitory pathways with loops, the mechanisms regulating the two types of plasticity remain poorly understood. A signaling pathway model of spines that express D1-type dopamine receptors was constructed to analyze the dynamic mechanisms of dopamine- and calcium-dependent plasticity. The model incorporated all major signaling molecules, including dopamine- and cyclic AMP-regulated phosphoprotein with a molecular weight of 32 kDa (DARPP32), as well as AMPA receptor trafficking in the post-synaptic membrane. Simulations with dopamine and calcium inputs reproduced dopamine- and calcium-dependent plasticity.

Further in silico experiments revealed that the positive feedback loop consisted of protein kinase A (PKA), protein phosphatase 2A (PP2A), and the phosphorylation site at threonine 75 of DARPP-32 (Thr75) served as the major switch for inducing LTD and LTP. Calcium input modulated this loop through the PP2B (phosphatase 2B)-CK1 (casein kinase 1)-Cdk5 (cyclin-dependent kinase 5)-Thr75 pathway and PP2A, whereas calcium and dopamine input activated the loop via PKA activation by cyclic AMP (cAMP). The positive feedback loop displayed robust bi-stable responses following changes in the reaction parameters. Increased basal dopamine levels disrupted this dopamine-dependent plasticity. The present model elucidated the mechanisms involved in bidirectional regulation of corticostriatal synapses and will allow for further exploration into causes and therapies for dysfunctions such as drug addiction. Rveview the complete article via the PLoS portal

Shaping the tree of DNA’s regulators (Broad Institute)

In each cell of the human body, more than six feet of DNA are carefully tucked into the tiny nucleus by wrapping around proteins called histones, resembling beads on a string. But histones are more than spools around which the DNA thread winds. Through chemical tags on their surface, histones can regulate activity of the genome, turning genes on or off by regulating how tightly DNA is compacted.

Scientists now recognize the growing importance of one family of enzymes with a role in this cellular dance. Histone deacetylases (HDACs) are enzymes that were originally discovered because of their roles in “epigenetic” modulation of genetic material — removing small chemical tags from histone proteins and thereby regulating the activity of certain genes. Today, scientists know that HDACs directly modify a large number of other proteins, suggesting they could play an even larger role in the cell.

There are 11 HDACs in humans, many originally characterized by Stuart Schreiber, director of the Chemical Biology Program at the Broad Institute of MIT and Harvard. These enzymes play central roles in development, physiology, and diseases like cancer, metabolic disease, and neurodegenerative disorders. Two drugs that target HDACs, known as HDAC inhibitors, have been approved for use in humans and more are in clinical testing. The Broad Institute portal provides complete study findings

Now-Generation Sequencing Conference - Cambridge Healthtech Institute (March 17-19 in San Diego)

Next-generation sequencing (NGS) has emerged as now-generation sequencing and has moved from the testing stage into production. Platform providers of second-generation systems have increased read length and throughput of their instruments, facilitated paired-end sequencing, and lowered the cost of sequencing. End-users from the basic and biomedical research community are making discoveries as rapidly as the bases are being sequenced. All agree, however, that with the implementation and maturation of any new technology there is a balancing act of cost-quality-quantity. What is your sequencing goal? The potential applications are as numerous as the samples to be analyzed. Each NGS platform is optimized for specific sequencing applications. Cambridge Healthtech Institute’s Fourth Annual Now-Generation Sequencing offers an unparalleled opportunity to compare and contrast the NGS platforms to best suit your research needs.

Next-generation sequencing (NGS) has energized the scientific community and captured the public’s attention. As we move into the new era of genomic sequencing, it’s important to quantify these new technological advances and answer the question…. What is the return on investment? In this exciting Plenary Session, join genomic thought-leaders from diverse backgrounds as they share their views on when and where they believe NGS’ ROI will first be realized. Visit the conference portal for the complete agenda and speaker bios

Inference of RhoGAP/GTPase regulation using single-cell morphological data from an RNAi screen

Biological networks are highly complex systems, consisting largely of enzymes that act as molecular switches to activate/inhibit downstream targets via post-translational modification. Computational techniques have been developed to perform signaling network inference using some high-throughput data sources, such as those generated from transcriptional and proteomic studies, but comparable methods have not been developed to use high-content morphological data, which are emerging principally from large-scale RNAi screens, to these ends. Here, we describe a systematic computational framework based on a classification model for identifying genetic interactions using high-dimensional single-cell morphological data from genetic screens, apply it to RhoGAP/GTPase regulation in Drosophila, and evaluate its efficacy.

Augmented by knowledge of the basic structure of RhoGAP/GTPase signaling, namely, that GAPs act directly upstream of GTPases, we apply our framework for identifying genetic interactions to predict signaling relationships between these proteins. We find that our method makes mediocre predictions using only RhoGAP single-knockdown morphological data, yet achieves vastly improved accuracy by including original data from a double-knockdown RhoGAP genetic screen, which likely reflects the redundant network structure of RhoGAP/GTPase signaling. We consider other possible methods for inference and show that our primary model outperforms the alternatives. This work demonstrates the fundamental fact that high-throughput morphological data can be used in a systematic, successful fashion to identify genetic interactions and, using additional elementary knowledge of network structure, to infer signaling relations. Visit the Genome Research portal for complete details

Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss

Gene transcription is associated with local changes in chromatin, both in nucleosome positions and in chemical modifications of the histones. Chromatin dynamics has mostly been studied on a single-gene basis. Those genome-wide studies that have been made primarily investigated steady-state transcription. However, three studies of genome-wide changes in chromatin during the transcriptional response to heat shock in the budding yeast Saccharomyces cerevisiae revealed nucleosome eviction in promoter regions but only minor effects in coding regions. Here, we describe the short-term response to nitrogen starvation in the fission yeast Schizosaccharomyces pombe. Nitrogen depletion leads to a fast induction of a large number of genes in S. pombe and is thus suitable for genome-wide studies of chromatin dynamics during gene regulation.

After 20 min of nitrogen removal, 118 transcripts were up-regulated. The distribution of regulated genes throughout the genome was not random; many up-regulated genes were found in clusters, while large parts of the genome were devoid of up-regulated genes. Surprisingly, this up-regulation was associated with nucleosome eviction of equal magnitudes in the promoters and in the coding regions. The nucleosome loss was not limited to induction by nitrogen depletion but also occurred during cadmium treatment. Furthermore, the lower nucleosome density persisted for at least 60 min after induction. Two highly induced genes,urg1+ and urg2+, displayed a substantial nucleosome loss, with only 20% of the nucleosomes being left in the coding region. We conclude that nucleosome loss during transcriptional activation is not necessarily limited to promoter regions. Review the abstract or order this article via the Genome Research portal

Regulation of Energy Homeostasis by Bombesin Receptor Subtype-3 (Cell Metabolism)

Bombesin receptor subtype 3 (BRS-3) is a G protein coupled receptor whose natural ligand is unknown. We developed potent, selective agonist (Bag-1, Bag-2) and antagonist (Bantag-1) ligands to explore BRS-3 function. BRS-3-binding sites were identified in the hypothalamus, caudal brainstem, and several midbrain nuclei that harbor monoaminergic cell bodies. Antagonist administration increased food intake and body weight, whereas agonists increased metabolic rate and reduced food intake and body weight. Prolonged high levels of receptor occupancy increased weight loss, suggesting a lack of tachyphylaxis.

BRS-3 agonist effectiveness was absent in Brs3^-/Y (BRS-3 null) mice but was maintained in Npy^-/-Agrp^-/-, Mc4r^-/-, Cnr1^-/-, and Lepr^db/db mice. In addition, Brs3^-/Y mice lost weight upon treatment with either a MC4R agonist or a CB1R inverse agonist. These results demonstrate that BRS-3 has a role in energy homeostasis that complements several well-known pathways and that BRS-3 agonists represent a potential approach to the treatment of obesity. Review the article and join the discussion via the Cell Metabolism portal

TGen finalizes alliance with Van Andel Research Institute (VARI)

The Translational Genomics Research Institute (TGen) announced the completion of a strategic alliance and affiliation agreement with the Van Andel Research Institute (VARI) that will maximize the research capabilities of both non-profit institutes. TGen expects the agreement to create a robust basic-science-to-translational delivery platform aimed at developing new tests and treatments for patient benefit.

"We are excited to align with a prominent institute like Van Andel, a partnership that I fully expect to yield greater scientific and economic returns for both Arizona and Michigan," said Dr. Jeffrey Trent, TGen's President and Research Director, a title he also now holds at VARI.

TGen remains an Arizona-based 501(c)(3) non-profit biomedical research organization, headquartered in Phoenix with an Arizona-centric board. VARI, based in Grand Rapids, Michigan, will be the organization's sole member. Since making an initial alliance announcement in February 2009, TGen worked with key Arizona partners to ratify any needed changes to funding or research agreements, including the Flinn Foundation, the Virginia G. Piper Charitable Trust, the Arizona Board of Regents, a number of the Valley's health care providers, and the State of Arizona. Visit the TGen news room for complete partnership details

Positioned and G/C capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions

Eukaryotic transcriptional regulation is mediated by the organization of nucleosomes in promoter regions. Most S. cerevisiae promoters have a highly stereotyped chromatin organization, where nucleosome-free regions (NFR) are flanked by well-ordered nucleosomes. We have found that yeast promoters fall into two classes differing in NFR sharpness, and that this distinction follows a known transcriptional dichotomy in yeast genes. A class of yeast promoters having well-defined NFRs are characterized by positioned patterns of poly(dA:dT) tracts with several novel features. First, poly(dA:dT) tracts are localized in a strand-dependent manner, with poly(dA) tracts lying proximal to transcriptional start sites and poly(dT) tracts lying distal, and collectively define a symmetry axis that is coincident with NFR centers.

Second, poly(dA:dT) tracts are preferentially "capped" by G:C residues on the terminus proximal to the symmetry axis. Both signature features co-vary with fine positional variations between NFRs, establishing a closely-knit relationship between poly(dA:dT) tracts, their capping patterns, and the central coordinates of NFRs. We found that these features are unique to promoters with well-defined NFRs, and that these promoters display significant difference between in vitro and in vivo nucleosome occupancy patterns. These observations are consistent with a model in which localized and G:C-capped poly(dA:dT) tracts initiate or facilitate the formation of NFRs at their center, possibly with chromatin remodeling and transcriptional machines involved.

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets (PLoS)

Many human diseases are related to each other through shared causes or even shared pathology. Knowledge of these relationships has long been exploited to treat similar diseases with the same therapies. However, most of the traditional approaches to discover these relationships have depended on subjective measures, such as similarity in symptoms, or incomplete knowledge, such as genes with mutations. Here we present the first approach integrating high-throughput datasets such as mRNA expression and large-scale protein-protein interaction networks to discover human disease relationships in a systematic and quantitative way. We discover 138 significant pathological similarities between 54 human diseases ranging from lung cancer, schizophrenia, and malaria.

We also discovered a set of common pathways and processes within the cell that are dysregulated in at least half of the diseases. We infer that these processes correspond to a common response of the human system to a disease state. Interestingly, we find that many of the proteins in these pathways are already known to be targets of existing drugs. In fact, the drugs corresponding to these proteins are known to treat significantly more diseases than expected by chance highlighting the importance of these common molecular pathological pathways as prime therapeutic opportunities. Review the complete abstract or order this report via the PLoS portal

A map of open chromatin in human pancreatic islets (Nature Genetics)

Tissue-specific transcriptional regulation is central to human disease. To identify regulatory DNA active in human pancreatic islets, we profiled chromatin by formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq). We identified ~80,000 open chromatin sites. Comparison of FAIRE-seq data from islets to that from five non-islet cell lines revealed ~3,300 physically linked clusters of islet-selective open chromatin sites, which typically encompassed single genes that have islet-specific expression.

We mapped sequence variants to open chromatin sites and found that rs7903146, a TCF7L2 intronic variant strongly associated with type 2 diabetes, is located in islet-selective open chromatin. We found that human islet samples heterozygous for rs7903146 showed allelic imbalance in islet FAIRE signals and that the variant alters enhancer activity, indicating that genetic variation at this locus acts in cis with local chromatin and regulatory changes. These findings illuminate the tissue-specific organization of cis-regulatory elements and show that FAIRE-seq can guide the identification of regulatory variants underlying disease susceptibility. Review the abstract in full via the Nature Genetics portal

A temporal precedence based clustering method for gene expression microarray data (BMC)

Time-course microarray experiments can produce useful data which can help in understanding the underlying dynamics of the system. Clustering is an important stage in microarray data analysis where the data is grouped together according to certain characteristics. The majority of clustering techniques are based on distance or visual similarity measures which may not be suitable for clustering of temporal microarray data where the sequential nature of time is important. We present a Granger causality based technique to cluster temporal microarray gene expression data, which measures the interdependence between two time-series by statistically testing if one time-series can be used for forecasting the other time-series or not.

A gene-association matrix is constructed by testing temporal relationships between pairs of genes using the Granger causality test. The association matrix is further analyzed using a graph-theoretic technique to detect highly connected components representing interesting biological modules. We test our approach on synthesized datasets and real biological datasets obtained for Arabidopsis thaliana. We show the effectiveness of our approach by analyzing the results using the existing biological literature. We also report interesting structural properties of the association network commonly desired in any biological system.

Experiments on synthesized and real microarray datasets show that our approach produces encouraging results. The method is simple in implementation and is statistically traceable at each step. The method can produce sets of functionally related genes which can be further used for reverse engineering of gene circuits. Visit the BMC Bioinformatics portal to review the abstract or order this report

TGen and Geisinger Health System Announce Partnership to Shape Future of Personalized Medicine

The Translational Genomics Research Institute (TGen) and Geisinger Health System announced the signing of a strategic research agreement that provides for a focused look at the gaps in clinical medicine where biomedical research can make a difference.

One of the first projects will focus on the causes of obesity, diabetes and other metabolic conditions. Researchers plan to look at the possible genetic reasons why so many Americans are overweight, and why diet, exercise and, specifically, bariatric surgery may fail to significantly reduce excess weight in some patients. TGen, a non-profit biomedical research institute based in Phoenix, will pair its genomic and proteomic research expertise with the clinical excellence and research expertise of Geisinger, a non-profit medical and insurance provider based in Danville, Pa. Geisinger’s strength is its integrated healthcare delivery model, nontransitory population and advanced electronic health record (EHR) with nearly two decades of data. In addition to providing the clinical underpinnings for the study of obesity, the data within the EHR will provide researchers the evidence they need to make discoveries in future projects centered on cancer and other serious diseases.

“Merging Geisinger’s wealth of clinical information with our genomic and proteomic expertise should provide researchers a richer framework for exploring the genetic origins of disease, and hopefully lead to improved treatments and outcomes,” said Dr. Jeffrey Trent, Ph.D., TGen’s President and Research Director. The TGen press portal offers complete partnership details

Finnish and Swiss researchers have determined the crystal structure of the ligand binding domain of a vascular endothelial growth factor (VEGF)

Cancer cells require access to blood and lymph vessels for invasive growth and metastasis. By releasing VEGFs, cancer cells stimulate the surrounding blood vessels to invade the cancerous tumor mass. Blocking this process is a new strategy to inhibit tumor growth.

VEGFs and their receptors have been identified as major targets for drug development in cancer therapy and the VEGF receptor that the groups analyzed is currently the most important target of such drugs. Professor Kari Alitalo's research group at the University of Helsinki discovered the VEGF-C growth factor in 1996 and found that it is involved in lymphatic vessel growth, cancer metastasis and, more recently, also in blood vessel growth in cancer.

The collaborative work published in PNAS by the two research teams provides significant new insights into VEGF receptor function, tells Dr. Veli-Matti Leppänen. The work was made possible by the long-standing interest and collaborative research of the binational team and the availability of excellent crystallography beamlines at the Swiss Synchrotron Light Source located at PSI, and it was supported by the European Union.

Finland invests €1.85 million in pan-European infrastructure for biomedical research

Finland has made its first specific commitment to the development of European biomedical research infrastructures (BMS ESFRIs) by supporting a joint pilot infrastructure project in bioinformatics (ELIXIR), biobanking (BBMRI) and translational research (EATRIS). The initial commitment of 1.85 M€ is to support preparation and pilot studies in 2010.

This funding is meant to ensure Finland's commitment to the building of these European infrastructures. The level of funding in the future years was left open as this depends on the outcome and structures that will be developed in the pilot phase.

The approach that Finland has selected is based on the realization that significant potential synergies may arise from infrastructures developed for biobanking, bioinformatics and translational medical research. Funding of 1 M€ is provided by the Ministry of Education through the Academy of Finland, with 0.85 M€ co-financing from the consortium consisting of the Institute for Molecular Medicine Finland (FIMM), CSC – IT Center for Science Ltd and the National Institute for Health and Welfare (THL).

This project is meant to ensure that Finnish scientists and institutions will continue to be active in the planning and implementation of the first wave of European BMS ESFRI infrastructures. There is particular interest to form links and synergies between the infrastructures, such as by linking sustainable infrastructure for biological information (ELIXIR) with biomedical samples and clinical, life-style and environmental data (BBMRI) as well as an opportunity to translate results to diagnostic and biomarker purposes (EATRIS).

UCLA Team Sequences Brain Cancer Cell Line (PLoS Genetics)

Researchers from the University of California at Los Angeles reported in PLoS Genetics that they have sequenced the genome of a glioblastoma multiforme brain cancer cell line. The team sequenced the GBM cell line, called U87MG, to about 30 times coverage. During their subsequent analyses, the team identified numerous SNPs, structural variants, translocations, and small insertions and deletions not found in the human reference genome — many affecting protein-coding sequences.

"This was the most thorough sequencing analysis of an individual cancer cell line that has been performed to date," senior author Stan Nelson, a genetics researcher and director of the UCLA Jonsson Comprehensive Cancer Center's gene expression shared resource, said in a statement. "Lots of biology is based on cell lines," Nelson told GenomeWeb Daily News, "but we have a rather incomplete view of what these cell lines are." Finding mutations within cell lines should provide researchers with an additional resource for putting findings based on these cell lines in context, he added.

Several genomic studies have focused on GBM, including sequencing work by members of The Cancer Genome Atlas. But, Nelson and his colleagues explained, the new paper represents the first time a GBM cell line has had its whole genome sequenced. The PLoS Genetics portal provides the complete study abstract

St. Jude, Washington University Launch Genome Project for Childhood Cancers

Researchers at St. Jude Children’s Research Hospital and the Washington University School of Medicine in St. Louis have launched the Pediatric Cancer Genome Project to sequence the genomes of at least 600 children with cancer over the next 3 years. The collaboration marks the first time that whole-genome sequencing will be used on a large scale to discover genetic changes driving pediatric cancers.

“This is the largest and most powerful single initiative in the 50-year history of St. Jude,” the research hospital’s director, Dr. William E. Evans, said at a press briefing announcing the project yesterday. “DNA is being sequenced as we speak,” he added.

“This is a new era for pediatric cancers,” NIH Director Dr. Francis Collins said at the briefing. “The study represents an opportunity to discover all the ways that a good cell in an innocent child goes wrong.”

The project—estimated to cost $65 million and funded by St. Jude—aims to discover the genetic origins of pediatric cancers while creating knowledge that can be used to improve the care of young people with these rare diseases. Early results could reveal new uses for available drugs, and, over the long term, lead to targeted agents for these cancers, the researchers said. New genetic signatures for classifying and treating patients are also anticipated. Knowing that a child has a subtype with a poor prognosis would allow physicians to select aggressive treatments early in the course of the disease. Similarly, doctors could safely withhold treatments from a patient who has a better prognosis, based on a genetic profile. Visit the NCI portal for complete study details

Gene Function Discovery: Guilt by Association (Carnegie Institution for Science)

Scientists have created a new computational model that can be used to predict gene function of uncharacterized plant genes with unprecedented speed and accuracy. The network, dubbed AraNet, has over 19,600 genes associated to each other by over 1 million links and can increase the discovery rate of new genes affiliated with a given trait tenfold. It is a huge boost to fundamental plant biology and agricultural research.

Despite immense progress in functional characterization of plant genomes, over 30% of the 30,000 Arabidopsis genes have not been functionally characterized yet. Another third has little evidence regarding their role in the plant.

“In essence, AraNet is based on the simple idea that genes that physically reside in the same neighborhood, or turn on in concert with one another are probably associated with similar traits,” explained corresponding author Sue Rhee at the Carnegie Institution’s Department of Plant Biology. “We call it guilt by association. Based on over 50 million scientific observations, AraNet contains over 1 million linkages of the 19,600 genes in the tiny, experimental mustard plant Arabidopsis thaliana. We made a map of the associations and demonstrated that we can use the network to propose that uncharacterized genes are linked to specific traits based on the strength of their associations with genes already known to be linked to those characteristics.” The Carnegie Institution for Science press room offers research findings

New computational tool for cancer treatment (SIB)

Researchers in the Molecular Modeling group at the SIB Swiss Institute of Bioinformatics and Dr. Benoît J. Van den Eynde's group at the Ludwig Institute for Cancer Research Ltd (LICR) Brussels Branch developed an approach for creating new IDO inhibitors by computer-assisted structure-based drug design. The study was presented in the January 2010 online issue of the Journal of Medicinal Chemistry.

The docking algorithm EADock, used for this project, was developed by the Molecular Modeling Group over the last eight years. It provides solutions for the "lock-and-key" problem, wherein the protein active site is regarded as a "lock", which can be fitted with a "key" (usually a small organic molecule) able to regulate its activity. Once an interesting molecule has been obtained, synthesis and laboratory experiments are necessary to confirm or reject the prediction. This algorithm will soon be made available to the scientific community worldwide.

The scientists obtained a high success rate. Fifty percent of the molecules designed in silico were active IDO inhibitors in vitro. Compounds that displayed activities in the low micromolar to nanomolar range, made them suitable for further testing in tumor cell experiments and for in vivo evaluation in mice. If these studies are successful, scientists can begin evaluating these new compounds in patients undergoing cancer-immunotherapy.

According to Olivier Michielin, Assistant Member at the Lausanne Branch of LICR and leader of the SIB Swiss Institute of Bioinformatics Molecular Modeling group, "This is a satisfactory proof of principle showing that computational techniques can produce very effective inhibitors for specific cancer targets with high yield. This is very encouraging for future drug developments in the academic environment." Visit the SIB press room for complete study findings