Edgetic perturbation models of human inherited disorders

Cellular functions are mediated through complex systems of macromolecules and metabolites linked through biochemical and physical interactions, represented in interactome models as ‘nodes' and ‘edges', respectively. Better understanding of genotype-to-phenotype relationships in human disease will require modeling of how disease-causing mutations affect systems or interactome properties. Here we investigate how perturbations of interactome networks may differ between complete loss of gene products (‘node removal') and interaction-specific or edge-specific (‘edgetic') alterations. Global computational analyses of ∼50 000 known causative mutations in human Mendelian disorders revealed clear separations of mutations probably corresponding to those of node removal versus edgetic perturbations. Experimental characterization of mutant alleles in various disorders identified diverse edgetic interaction profiles of mutant proteins, which correlated with distinct structural properties of disease proteins and disease mechanisms. Edgetic perturbations seem to confer distinct functional consequences from node removal because a large fraction of cases in which a single gene is linked to multiple disorders can be modeled by distinguishing edgetic network perturbations. Edgetic network perturbation models might improve both the understanding of dissemination of disease alleles in human populations and the development of molecular therapeutic strategies

Diastereospecific Bis-alkoxycarbonylation of 1,2-Disubstituted Olefins Catalyzed by Aryl α-Diimine Palladium(II) Catalysts

Readily synthesized aryl α-diimine derivatives have been used as efficient ligands for the palladium-catalyzed oxidative bis-alkoxycarbonylation reaction of 1,2-disubstituted olefins. The most active catalyst A was formed in situ from bis-(2,6-dimethylphenyl)-2,3-dimethyl-1,4-diazabutadiene and Pd(TFA)2 (TFA=trifluoroacetate). This catalytic system was able to selectively convert 1,2-disubstituted olefins into 2,3-disubstituted-succinic diesters with total diastereospecificity, in good yields (up to 97%) with 2 mol% of catalyst loading, under mild reaction conditions (4 bar of CO at 20 °C in presence of p- toluenesulfonic acid as additive and p-benzoquinone as oxidant). The optimized reaction conditions could be successfully applied to 1,2-disubstituted aromatic, aliphatic, cyclic olefins and to unsaturated fatty acid methyl esters, employing methanol or benzyl alcohol as nucleophiles. The use of the bulky, less reactive isopropyl alcohol has allowed to better understand the mechanisms involved in the catalytic process. The geometry of the carbonylated products can be explained as a consequence of a concerted syn addition of the Pd-alkoxycarbonyl moiety to the olefin C=C bond. Catalyst A was isolated, characterized and analyzed by single crystal X-ray diffraction analysis. (Figure presented.)

An antibiotic selection marker for nematode transgenesis

We have developed a nematode transformation vector carrying the bacterial neomycin resistance gene (NeoR) and shown that it could confer resistance to G-418 on both wild-type Caenorhabditis elegans and C. briggsae. This selection system allows hands-off maintenance and enrichment of transgenic worms carrying non-integrated transgenes on selective plates. We also show that this marker can be used for Mos1-mediated single-copy insertion in wild-type genetic backgrounds (MosSCI-biotic)

Improving Drug Discovery by Nucleic Acid Delivery in Engineered Human Microlivers

The liver plays a central role in metabolism; however, xenobiotic metabolism variations between human hepatocytes and those in model organisms create challenges in establishing functional test beds to detect the potential drug toxicity and efficacy of candidate small molecules. In the emerging areas of RNA interference, viral gene therapy, and genome editing, more robust, long-lasting, and predictive human liver models may accelerate progress. Here, we apply a new modality to a previously established, functionally stable, multi-well bioengineered microliver—fabricated from primary human hepatocytes and supportive stromal cells—in order to advance both small molecule and nucleic acid therapeutic pipelines. Specifically, we achieve robust and durable gene silencing in vitro to tune the human metabolism of small molecules, and demonstrate its capacity to query the potential efficacy and/or toxicity of candidate therapeutics. Additionally, we apply this engineered platform to test siRNAs designed to target hepatocytes and impact human liver genetic and infectious diseases. Mancio-Silva et al. show that nucleic acid-mediated silencing of primary human hepatocytes can be leveraged in an in vitro engineered human liver model to fine-tune metabolism and to assess safety and efficacy of RNAi-based therapeutics.National Cancer Institute (Grant P30-CA14051

C. elegans GLA-3 is a novel component of the MAP kinase MPK-1 signaling pathway required for germ cell survival

During oocyte development in Caenorhabditis elegans, approximately half of all developing germ cells undergo apoptosis. While this process is evolutionarily conserved from worms to humans, the regulators of germ cell death are still largely unknown. In a genetic screen for novel genes involved in germline apoptosis in Caenorhabditis elegans, we identified and cloned gla-3. Loss of gla-3 function results in increased germline apoptosis and reduced brood size due to defective pachytene exit from meiosis I. gla-3 encodes a TIS11-like zinc-finger-containing protein that is expressed in the germline, from the L4 larval stage to adulthood. Biochemical evidence and genetic epistasis analysis revealed that GLA-3 participates in the MAPK signaling cascade and directly interacts with the C. elegans MAPK MPK-1, an essential meiotic regulator. Our results show that GLA-3 is a new component of the MAPK cascade that controls meiotic progression and apoptosis in the C. elegans germline and functions as a negative regulator of the MAPK signaling pathway during vulval development and in muscle cells

C. elegans ORFeome Version 3.1: Increasing the Coverage of ORFeome Resources With Improved Gene Predictions

The first version of the Caenorhabditis elegans ORFeome cloning project, based on release WS9 of Wormbase (August 1999), provided experimental verifications for ∼55% of predicted protein-encoding open reading frames (ORFs). The remaining 45% of predicted ORFs could not be cloned, possibly as a result of mispredicted gene boundaries. Since the release of WS9, gene predictions have improved continuously. To test the accuracy of evolving predictions, we attempted to PCR-amplify from a highly representative worm cDNA library and Gateway-clone ∼4200 ORFs missed earlier and for which new predictions are available in WS100 (May 2003). In this set we successfully cloned 63% of ORFs with supporting experimental data (“touched” ORFs), and 42% of ORFs with no supporting experimental evidence (“untouched” ORFs). Approximately 2000 full-length ORFs were cloned in-frame, 13% of which were corrected in their exon/intron structure relative to WS100 predictions. In total, ∼12,500 C. elegans ORFs are now available as Gateway Entry clones for various reverse proteomics (ORFeome v3.1). This work illustrates why the cloning of a complete C. elegans ORFeome, and likely the ORFeomes of other multicellular organisms, needs to be an iterative process that requires multiple rounds of experimental validation together with gradually improving gene predictions