Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings

A national workgroup convened by the Centers for Disease Control and Prevention identified principles and made recommendations for standardizing the description of sequence data contained within the variant file generated during the course of clinical next-generation sequence analysis for diagnosing human heritable conditions. The specifications for variant files were initially developed to be flexible with regard to content representation to support a variety of research applications. This flexibility permits variation with regard to how sequence findings are described and this depends, in part, on the conventions used. For clinical laboratory testing, this poses a problem because these differences can compromise the capability to compare sequence findings among laboratories to confirm results and to query databases to identify clinically relevant variants. To provide for a more consistent representation of sequence findings described within variant files, the workgroup made several recommendations that considered alignment to a common reference sequence, variant caller settings, use of genomic coordinates, and gene and variant naming conventions. These recommendations were considered with regard to the existing variant file specifications presently used in the clinical setting. Adoption of these recommendations is anticipated to reduce the potential for ambiguity in describing sequence findings and facilitate the sharing of genomic data among clinical laboratories and other entities.

The Arf GAP CNT-2 regulates the apoptotic fate in C. elegans asymmetric neuroblast divisions

During development, all cells make the decision to live or die. Although the molecular mechanisms that execute the apoptotic program are well defined, less is known about how cells decide whether to live or die. In C. elegans, this decision is linked to how cells divide asymmetrically [1, 2]. Several classes of molecules are known to regulate asymmetric cell divisions in metazoans, yet these molecules do not appear to control C. elegans divisions that produce apoptotic cells [3]. We identified CNT-2, an Arf GTPase-activating protein (GAP) of the AGAP family, as a novel regulator of this type of neuroblast division. Loss of CNT-2 alters daughter cell size and causes the apoptotic cell to adopt the fate of its sister cell, resulting in extra neurons. CNT-2's Arf GAP activity is essential for its function in these divisions. The N terminus of CNT-2, which contains a GTPase-like domain that defines the AGAP class of Arf GAPs, negatively regulates CNT-2's function. We provide evidence that CNT-2 regulates receptor-mediated endocytosis and consider the implications of its role in asymmetric cell divisions.

Hepatitis A virus (HAV) proteinase 3C inhibits HAV IRES-dependent translation and cleaves the polypyrimidine tract-binding protein

Hepatitis A virus (HAV) infection is still an important issue worldwide. A distinct set of viruses encode proteins that enhance viral cap-independent translation initiation driven by an internal ribosome entry site (IRES) and suppress cap-dependent host translation. Unlike cytolytic picornaviruses, replication of HAV does not cause host cell shut off, and it has been questioned whether HAV proteins interfere with its own and/or host translation. HAV proteins were coexpressed in Huh-7 cells with reporter genes whose translation was initiated by either cap-dependent or cap-independent mechanisms. Among the proteins tested, HAV proteinase 3C suppressed viral IRES-dependent translation. Furthermore, 3C cleaved the polypyrimidine tract-binding protein (PTB) whose interaction with the HAV IRES had been demonstrated previously. The combined results suggest that 3C-mediated cleavage of PTB might be involved in down-regulation of viral translation to give way to subsequent viral genome replication.

Abstract LB-126: A pooled shRNA screen for erlotinib sensitizers in Kras-mutant non-small cell lung cancer

Erlotinib is a small-molecule inhibitor of the epithelial growth factor receptor (EGFR) that provides a survival benefit in patients with chemoresistant non-small cell lung cancer (NSCLC). In the second and third line setting, patients whose tumors harbor activating mutations in Kras showed less benefit than patients with tumors harboring wild type Kras.

To identify genes whose inhibition sensitizes Kras-mutant NSCLC cells to erlotinib, we performed a whole-genome pooled-shRNA screen and identified 337 shRNAs that were selectively depleted in erlotinib-treated cells. We subsequently validated 148 of the top 200 hits in an siRNA-based viability assay and selected 37 hits for further analysis. We are currently characterizing these hits in a panel of ∼10 additional NSCLC lines to identify targets with broad cell line activity that synergize with erlotinib to induce apoptosis. Our current understanding of the relationships between our top hits and erlotinib sensitivity will be discussed.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-126.

Discovering cancer genes by integrating network and functional properties

BACKGROUND

Identification of novel cancer-causing genes is one of the main goals in cancer research. The rapid accumulation of genome-wide protein-protein interaction (PPI) data in humans has provided a new basis for studying the topological features of cancer genes in cellular networks. It is important to integrate multiple genomic data sources, including PPI networks, protein domains and Gene Ontology (GO) annotations, to facilitate the identification of cancer genes.

METHODS

Topological features of the PPI network, as well as protein domain compositions, enrichment of gene ontology categories, sequence and evolutionary conservation features were extracted and compared between cancer genes and other genes. The predictive power of various classifiers for identification of cancer genes was evaluated by cross validation. Experimental validation of a subset of the prediction results was conducted using siRNA knockdown and viability assays in human colon cancer cell line DLD-1.

RESULTS

Cross validation demonstrated advantageous performance of classifiers based on support vector machines (SVMs) with the inclusion of the topological features from the PPI network, protein domain compositions and GO annotations. We then applied the trained SVM classifier to human genes to prioritize putative cancer genes. siRNA knock-down of several SVM predicted cancer genes displayed greatly reduced cell viability in human colon cancer cell line DLD-1.

CONCLUSION

Topological features of PPI networks, protein domain compositions and GO annotations are good predictors of cancer genes. The SVM classifier integrates multiple features and as such is useful for prioritizing candidate cancer genes for experimental validations.

UNC-97/PINCH is involved in the assembly of integrin cell adhesion complexes in Caenorhabditis elegans body wall muscle

UNC-97/PINCH is an evolutionarily conserved protein that contains five LIM domains and is located at cell-extracellular matrix attachment sites known as cell adhesion complexes. To understand the role of UNC-97/PINCH in cell adhesion, we undertook a combined genetic and cell biological approach to identify the steps required to assemble cell adhesion complexes in Caenorhabditis elegans. First, we have generated a complete loss of function mutation in the unc-97 coding region. unc-97 null mutants arrest development during embryogenesis and reveal that the myofilament lattice and its attachment structures, which include PAT-4/ILK (integrin-linked kinase) and integrin fail to assemble into properly organized arrays. Although in the absence of UNC-97/PINCH, PAT-4/ILK and integrin fail to organize normally, they are capable of colocalizing together at the muscle cell membrane. Alternatively, in integrin and pat-4 mutants, UNC-97/PINCH fails to localize to the muscle cell membrane and instead is found diffusely throughout the muscle cell cytoplasm. In agreement with mammalian studies, we show that LIM domain 1 of UNC-97/PINCH is required for its interaction with PAT-4/ILK in yeast two-hybrid assays. Additionally, we find, by LIM domain deletion analysis, that LIM1 is required for the localization of UNC-97/PINCH to cell adhesion complexes. Our results provide evidence that UNC-97/PINCH is required for the development of C. elegans and is required for the formation of integrin based adhesion structures.

The C. elegans MELK ortholog PIG-1 regulates cell size asymmetry and daughter cell fate in asymmetric neuroblast divisions

In the nematode Caenorhabditis elegans, neurons are generated from asymmetric divisions in which a mother cell divides to produce daughters that differ in fate. Here, we demonstrate that the gene pig-1 regulates the asymmetric divisions of neuroblasts that divide to produce an apoptotic cell and either a neural precursor or a neuron. In pig-1 mutants, these neuroblasts divide to produce daughters that are more equal in size, and their apoptotic daughters are transformed into their sisters, leading to the production of extra neurons. PIG-1 is orthologous to MELK, a conserved member of the polarity-regulating PAR-1/Kin1/SAD-1 family of serine/threonine kinases. Although MELK has been implicated in regulating the cell cycle, our data suggest that PIG-1, like other PAR-1 family members, regulates cell polarity.

Multiple Wnts and frizzled receptors regulate anteriorly directed cell and growth cone migrations in Caenorhabditis elegans

A set of conserved molecules guides axons along the metazoan dorsal-ventral axis. Recently, Wnt glycoproteins have been shown to guide axons along the anterior-posterior (A/P) axis of the mammalian spinal cord. Here, we show that, in the nematode Caenorhabditis elegans, multiple Wnts and Frizzled receptors regulate the anterior migrations of neurons and growth cones. Three Wnts are expressed in the tail, and at least one of these, EGL-20, functions as a repellent. We show that the MIG-1 Frizzled receptor acts in the neurons and growth cones to promote their migrations and provide genetic evidence that the Frizzleds MIG-1 and MOM-5 mediate the repulsive effects of EGL-20. While these receptors mediate the effects of EGL-20, we find that the Frizzled receptor LIN-17 can antagonize MIG-1 signaling. Our results indicate that Wnts play a key role in A/P guidance in C. elegans and employ distinct mechanisms to regulate different migrations.

Variability signatures distinguish verbal from nonverbal counting for both large and small numbers

Humans appear to share with animals a nonverbal counting process. In a nonverbal counting condition, subjects pressed a key a numeral-specified number of times, while saying "the" at every press. The mean number of presses increased as a power function of the target number, with a constant coefficient of variation (c.v.), both within and beyond the proposed subitizing range (1-4 or 5), suggesting small numbers are represented on the same continuum as larger numbers and subject to the same noise process (scalar variability). By contrast, when subjects counted their presses out loud as fast as they could, the c.v. decreased as the inverse square root of the target value (binomial variability instead of scalar variability). The unexpected power-law relation between target value and mean number of presses in nonverbal counting suggests a new hypothesis about the development of the function relating number symbols to mental magnitudes.

A fatigue life analysis of small fragment screws

OBJECTIVES

To conduct a comparative fatigue analysis of several commonly used small fragment screws.

DESIGN

Biomechanical laboratory study.

SETTING

Research laboratory.

MAIN OUTCOME MEASUREMENTS

A fatigue life analysis of seven different types of small fragment screws was conducted using a Wohler fatigue-testing machine. Four different types of 3.5-millimeter cortical screws were subjected to fatigue analysis. These included solid stainless steel screws from Synthes Ltd. (core diameter 2.4 millimeters), Zimmer Inc. (core diameter 2.4 millimeter), and Smith and Nephew Richards Inc. (core diameter 2.4 millimeters) and cannulated stainless steel screws from Synthes Ltd. (core diameter 2.5 millimeters). In addition, three types of 4.0-millimeter cancellous screws were tested. These included stainless steel screws from Synthes Ltd. (core diameter 1.9 millimeters), titanium screws from Synthes Ltd. (core diameter 2.0 millimeters), and titanium alloy screws from DePuy-Ace (core diameter 2.8 millimeters). Fatigue lives, as reflected by mean cycles to failure, were compared.

RESULTS

The four types of cortical screws had longer fatigue lives than the Synthes cancellous screws did ( p < 0.001) but shorter fatigue lives than the DePuy-Ace cancellous screws did ( p < 0.0001). Among the cortical screws, the cannulated and solid Synthes screws and the solid Zimmer screws did not differ statistically. The Smith and Nephew Richards cortical screws failed at statistically fewer cycles than the Synthes solid and cannulated cortical screws did ( p < 0.003) but did not statistically differ from the Zimmer screws. The DePuy-Ace titanium alloy cancellous screw had the longest fatigue life of the tested implants by a large margin ( p < 0.0001). The Synthes pure titanium and stainless steel cancellous screws did not significantly differ.

CONCLUSIONS

This analysis supports core diameter as the principal factor determining fatigue life as the results paralleled implant geometry. This design modification to improve bending and fatigue strength may come at a price to pullout strength, however, because of a decreased major-to-minor diameter and increased pitch. Cortical screws differed in fatigue performance despite identical dimensions, presumably highlighting the importance of implant processing and machining. Cannulated cortical screws performed well relative to solid screws, thereby supporting their clinical use. Pure titanium and stainless steel cancellous screws performed similarly in fatigue despite differing material properties, presumably because of geometric design differences. This report highlights some of the differences in the in vitro fatigue performance among several commonly used small fragment screws.

Effects of ENU dosage on mouse strains

The germline supermutagen, N-ethyl-N-nitrosourea (ENU), has a variety of effects on mice. ENU is a toxin and carcinogen as well as a mutagen, and strains differ in their susceptibility to its effects. Therefore, it is necessary to determine an appropriate mutagenic, non-toxic dose of ENU for strains that are to be used in experiments. In order to provide some guidance, we have compiled data from a number of laboratories that have exposed male mice from inbred and non-inbred strains or their F(1) hybrids to ENU. The results show that most F(1) hybrid animals tolerate ENU well, but that inbred strains of mice vary in their longevity and in their ability to recover fertility after treatment with ENU.

Mechanical properties of small fragment screws

For many years, stainless steel small fragment screws have been produced by one manufacturer. Recently, other implant makers have begun offering similar stainless steel screws. In addition, screw geometry and material composition have been modified in an attempt to produce screws for a wide range of clinical situations. This study compared the mechanical properties of several commonly used small fragment screws. Seven sets of screws were tested mechanically, including three brands of geometrically identical standard stainless steel cortical screws and one brand each of cannulated stainless steel cortical screws, titanium cortical screws, stainless steel cancellous screws, and bioabsorbable polylactic acid screws. Screws from each group were tested for pullout strength, torque to failure, and three-point bending to failure. There were no differences in the mechanical properties of the identical 3.5-mm standard stainless steel cortical screws. No difference in pullout strength was found between the five sets of cortical screws. However, the cancellous screws had 4% to 24% less pullout strength. Torsion tests showed that cannulated stainless steel cortical, titanium cortical screws, stainless steel cancellous screws, and polylactic acid screws failed at significantly less torque than did standard stainless steel cortical screws. Standard stainless steel cortical screws had the highest mean yield point and maximal load at failure of all screws in three-point bending. Other metal screws had lower yield strength and maximal load at failure than did the standard stainless steel cortical screws, and polylactic acid screws had the least bending strength.

The changing landscape of health care financing and delivery: how are rural communities and providers responding?

Rural communities have not kept pace with the recent dramatic changes in health care financing and organization. However, the Medicare provisions in the Balanced Budget Act of 1997 will require rural providers to participate in the new systems. Case studies revealed the degree of readiness for change in six rural communities and charted their progress along a continuum, as reflected in three sets of activities: the development of networking; the creation of new strategies for managing patient care; and the adoption of new methods for contracting with health insurers. Some communities had constructed highly integrated systems, whereas others were just beginning to change their billing practices; a few were signing contracts for capitated care, in contrast to those that were resisting discounts in current fee structures. These six rural areas still have considerable ground to cover before their health care organization and financing reach the levels achieved by urban communities.

Rural hospitals and the local economy: a needed extension and refinement of existing empirical research

The relationship between the health care sector and the rural economy is of increasing importance. Much additional research is needed to fully understand this relationship and to address some of the limitations of the modest amount of research that already exists. In this study, data from Nebraska were used to create a four-part typology of rural hospitals. Input-output analysis was used to assess the economic effects of each type of hospital on the local economy and to simulate the effects of three different changes or scenarios: an increase or decrease in hospital utilization; the elimination of local purchases of nonlabor inputs; and a change in the mix or configuration of services provided. While the hospital is an important contributor to local economies, this contribution is not constant across hospital types. The total job-related effects ranged from 77 jobs for the smallest type of rural hospital to 1,332 for the largest type. Service and trade (retail plus wholesale) are the two sectors of the local economy most heavily influenced by the presence of a hospital. In today's changing and challenging environment, there is a great need for researchers to create and evaluate the economic effects of a variety of relevant and realistic scenarios (other than hospital closure).

Conserved and distinct roles of kreisler in regulation of the paralogous Hoxa3 and Hoxb3 genes

During anteroposterior patterning of the developing hindbrain, the anterior expression of 3′ Hox genes maps to distinct rhombomeric boundaries and, in many cases, is upregulated in specific segments. Paralogous genes frequently have similar anterior boundaries of expression but it is not known if these are controlled by common mechanisms. The expression of the paralogous Hoxa3 and Hoxb3 genes extends from the posterior spinal cord up to the rhombomere (r) 4/5 boundary and both genes are upregulated specifically in r5. However, in this study, we have found that Hoxa3 expression is also upregulated in r6, showing that there are differences in segmental expression between paralogues. We have used transgenic analysis to investigate the mechanisms underlying the pattern of segmental expression of Hoxa3. We found that the intergenic region between Hoxa3 and Hoxa4 contains several enhancers, which summed together mediate a pattern of expression closely resembling that of the endogenous Hoxa3 gene. One enhancer specifically directs expression in r5 and r6, in a manner that reflects the upregulation of the endogenous gene in these segments. Deletion analysis localized this activity to a 600 bp fragment that was found to contain a single high-affinity binding site for the Maf bZIP protein Krml1, encoded by the kreisler gene. This site is necessary for enhancer activity and when multimerized it is sufficient to direct a kreisler-like pattern in transgenic embryos. Furthermore the r5/r6 enhancer activity is dependent upon endogenous kreisler and is activated by ectopic kreisler expression. This demonstrates that Hoxa3, along with its paralog Hoxb3, is a direct target of kreisler in the mouse hindbrain. Comparisons between the Krml1-binding sites in the Hoxa3 and Hoxb3 enhancers reveal that there are differences in both the number of binding sites and way that kreisler activity is integrated and restricted by these two control regions. Analysis of the individual sites revealed that they have different requirements for mediating r5/r6 and dorsal roof plate expression. Therefore, the restriction of Hoxb3 to r5 and Hoxa3 to r5 and r6, together with expression patterns of Hoxb3 in other vertebrate species suggests that these regulatory elements have a common origin but have later diverged during vertebrate evolution.

Segmental regulation of Hoxb-3 by kreisler

Hox genes control regional identity during segmentation of the vertebrate hindbrain into rhombomeres. Here we use transgenic analysis to investigate the upstream mechanisms for regulation of Hoxb-3 in rhombomere(r)5. We identified enhancers from the mouse and chick genes sufficient for r5-restricted expression. Sequence comparisons revealed two blocks of similarity (of 19 and 45 base pairs), which each contain in vitro binding sites for the kreisler protein (Kmrl1), a Maf/b-Zip protein expressed in r5 and r6 (ref. 4). Both sites are required for r5 activity, suggesting that Hoxb-3 is a direct target of kreisler. Multimers of the 19-base-pair (bp) block recreate a Krml1-like pattern in r5/r6, but the 45-bp block mediates expression only in r5. Therefore elements within the 45-bp block restrict the response to Krml1. We identified additional sequences that contain an Ets-related activation site, required for both the activation and restriction to r5. These studies demonstrate that Krml1 directly activates expression of Hoxb-3 in r5 in combination with an Ets-related activation site, and suggest that kreisler plays a primary role in regulating segmental identity through Hox genes.

Correction of coxa vara in childhood. The use of Pauwels' Y-shaped osteotomy

The long-term results following the correction of coxa vara by Pauwels' Y-shaped intertrochanteric osteotomy have been evaluated in 14 children. Ten of the children had unilateral hip disease and were otherwise normal while four had bilateral hip disease due to generalised skeletal dysplasias. In each case, the growth plate was vertical, the femoral head was displaced inferiorly and there were abnormalities in the metaphysis of the femoral neck. The results indicate that this osteotomy provides lasting correction of the deformity, regardless of the cause, as long as the inclination of the growth plate is corrected to 40 degrees or less and adequate support is provided for the metaphyseal defect and the displaced femoral head.

Interaction of a developmentally regulated DNA-binding factor with sites flanking two different fruit-ripening genes from tomato

To investigate mechanisms that control fruit development, we have begun experiments to identify proteins that control gene expression during tomato fruit ripening. We focused on the regulation of two different genes, E4 and E8, whose transcription is coordinately activated at the onset of fruit ripening. We report here that a DNA-binding protein specifically reacts with similar sequences flanking the E4 and E8 genes. The E4 binding site is at position -34 to -18 and, therefore, overlaps the region (TATA box) that in many eukaryotic genes serves to determine the efficiency and initiation site of transcription. In contrast, the E8 binding site is distal, located at -936 to -920 relative to the start of E8 gene transcription. Gel electrophoresis mobility retardation experiments indicate that the DNA binding activity that interacts with these two sites increases at the onset of fruit ripening. Taken together, these results suggest that this DNA-binding protein may function to coordinate E4 and E8 gene expression during fruit ripening.

Optimized Monier-Williams method for determination of sulfites in foods: collaborative study

A collaborative study was conducted of the Food and Drug Administration (FDA)-optimized Monier-Williams method for determining sulfites in foods. Twenty-one industry and government laboratories participated in the study, which was jointly sponsored by the National Food Processors Association and FDA. Familiarization samples were shipped to each collaborator. Collaborators were permitted to proceed to the main study only after they demonstrated ability to perform the method to ensure that the study tested the performance of the method itself and not that of the individual laboratories. The study design involved 3 food matrixes (hominy, fruit juice, and protein [seafood]). Each matrix was prepared at 3 sulfite levels--the regulatory level, half the regulatory level, twice the regulatory level--and as a blank. All test samples were analyzed as blind duplicates, which gave each collaborator a total of 24 test portions. Collaborative recoveries gave a reproducibility (among-laboratories) coefficient of variation that ranged from 15.5 to 26.6% for sulfite determined as SO2 by weight in the 3 foods at the 10 ppm level. The optimized Monier-Williams method has been approved interim official first action to replace the AOAC modified Monier-Williams method, 20.123-20.125.

Regulation of gene expression by ethylene during Lycopersicon esculentum (tomato) fruit development

We have investigated the regulation of gene expression by the plant hormone ethylene by cloning mRNAs that accumulate in unripe tomato fruit (Lycopersicon esculentum) exposed to exogenous ethylene. The response to exogenous ethylene is rapid; within 30-120 min we detect an increase in the cloned mRNA concentrations. DNA sequence analysis indicates that one of the ethylene-inducible genes is related to a gene encoding wound-inducible proteinase inhibitor I. We have measured ethylene production during fruit development and detect low basal levels in unripe fruit and much higher levels in ripening fruit. Blot hybridization experiments show that expression of the cloned genes is developmentally regulated by ethylene during fruit ripening: the mRNAs produced by these genes are more abundant in ripe fruit than in unripe fruit, and this mRNA accumulation is repressed by a competitive inhibitor of ethylene action, norbornadiene. However, during fruit development some of the cloned mRNAs begin to accumulate when ethylene production is at a basal level, whereas other mRNAs begin to accumulate later when the endogenous ethylene concentration increases, suggesting that gene expression during fruit development can be activated by ethylene in two ways. In some cases gene expression is primarily activated by an increase in sensitivity to basal ethylene levels, whereas in other cases it may be regulated by an increase in ethylene concentration.

Purification and characterization of a transcription factor that confers promoter specificity to human RNA polymerase I

A whole-cell HeLa extract was fractionated into two components required for accurate in vitro transcription of human rRNA. One fraction contained endogenous RNA polymerase I, and the second component contained a factor (SL1) that confers promoter selectivity to RNA polymerase I. Analysis of mutant templates suggests that the core control element of the rRNA promoter is required for activation of transcription by SL1. We purified SL1 approximately 100,000-fold by column chromatography and have shown that the addition of SL1 can reprogram the otherwise nonpermissive mouse transcription system to recognize and initiate accurate RNA synthesis from human rDNA. Antibodies raised against SL1 bind preferentially to a protein localized in the nucleolus of primate cells and specifically inhibit in vitro transcription initiating from the human rRNA promoter. By contrast, anti-SL1 does not react with the nucleolus of rodent cells and has no effect on the in vitro synthesis of mouse rRNA by a transcription system derived from mouse cells. These findings suggest that SL1 is a selectivity factor present in the nucleolus that imparts promoter recognition to RNA polymerase I and that can discriminate between rRNA promoters from different species.