Identification of auxins by a chemical genomics approach

Thirteen auxenic compounds were discovered in a screen of 10 000 compounds for auxin-like activity in Arabidopsis roots. One of the most potent substances was 2-(4-chloro-2-methylphenoxy)-N-(4-H-1,2,4-triazol-3-yl)acetamide (WH7) which shares similar structure to the known auxenic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). A selected set of 20 analogues of WH7 was used to provide detailed information about the structure-activity relationship based on their efficacy at inhibiting and stimulating root and shoot growth, respectively, and at induction of gene expression. It was shown that WH7 acts in a genetically defined auxin pathway. These small molecules will extend the arsenal of substances that can be used to define auxin perception site(s) and to dissect subsequent signalling events.     

Identification of metastasis genes by a functional genomics approach

Comment on: Gumireddy K, et al. Nat Cell Biol 2009; 11:1297-304.     

PPAR gamma as a metabolic regulator: insights from genomics and pharmacology

Since its identification in the early 1990 s, peroxisome-proliferator-activated receptor gamma (PPAR gamma), a nuclear hormone receptor, has attracted tremendous scientific and clinical interest. The role of PPAR gamma in macronutrient metabolism has received particular attention, for three main reasons: first, it is the target of the thiazolidinediones (TZDs), a novel class of insulin sensitisers widely used to treat type 2 diabetes; second, it plays a central role in adipogenesis; and third, it appears to be primarily involved in regulating lipid metabolism with predominantly secondary effects on carbohydrate metabolism, a notion in keeping with the currently in vogue 'lipocentric' view of diabetes. This review summarises in vitro studies suggesting that PPAR gamma is a master regulator of adipogenesis, and then considers in vivo findings from use of PPAR gamma agonists, knockout studies in mice and analysis of human PPAR gamma mutations/polymorphisms.     

Chemical genomics: a systematic approach in biological research and drug discovery

The knowledge of complete sequences of different organisms is dramatically changing the landscape of biological research and pharmaceutical development. We are experiencing a transition from a trial-and-error approach in traditional biological research and natural product drug discovery to a systematic operation in genomics and target-specific drug design and selection. Small, cell-permeable and target-specific chemical ligands are particularly useful in systematic genomic approaches to study biological questions. On the other hand, genomic sequence information, comparative and structural genomics, when combined with the cutting edge technologies in synthetic chemistry and ligand screening/identification, provide a powerful way to produce target-specific and/or function-specific chemical ligands and drugs. Chemical genomics or chemogenomics is a new term that describes the development of target-specific chemical ligands and the use of such chemical ligands to globally study gene and protein functions. We anticipate that chemical genomics plays a critical role in the genomic age of biological research and drug discovery.     

Emerging role of cytokinin as a regulator of cellular differentiation

Perhaps the most amazing feature of plants is their ability to grow and regenerate for years, sometimes even centuries. This fascinating characteristic is achieved thanks to the activity of stem cells, which reside in the shoot and root apical meristems. Stem cells function as a reserve of undifferentiated cells to replace organs and sustain postembryonic plant growth. To maintain meristem function, stem cells have to generate new cells at a rate similar to that of cells leaving the meristem and differentiating, thus achieving a balance between cell division and cell differentiation. Recent findings have improved our knowledge on the molecular mechanisms necessary to establish this balance and reveal a fundamental signaling role for the plant hormone cytokinin. Evidence has been provided to show that in the root meristem cytokinin acts in defined developmental domains to control cell differentiation rate, thus controlling root meristem size.     

Genotype first: Clinical genomics research through a reverse phenotyping approach

1. Download : Download high-res image (77KB)
2. Download : Download full-size image

     

Autoimmune regulator, Aire, is a novel regulator of chondrocyte differentiation

Chondrocyte differentiation is controlled by various regulators, such as Sox9 and Runx2, but the process is complex. To further understand the precise underlying molecular mechanisms of chondrocyte differentiation, we aimed to identify a novel regulatory factor of chondrocyte differentiation using gene expression profiles of micromass-cultured chondrocytes at different differentiation stages. From the results of microarray analysis, the autoimmune regulator, Aire, was identified as a novel regulator. Aire stable knockdown cells, and primary cultured chondrocytes obtained from Aire^−/− mice, showed reduced mRNA expression levels of chondrocyte-related genes. Over-expression of Aire induced the early stages of chondrocyte differentiation by facilitating expression of Bmp2. A ChIP assay revealed that Aire was recruited on an Airebinding site (T box) in the Bmp2 promoter region in the early stages of chondrocyte differentiation and histone methylation was modified. These results suggest that Aire can facilitate early chondrocyte differentiation by expression of Bmp2 through altering the histone modification status of the promoter region of Bmp2.     

Identification of cold-shock protein RBM3 as a possible regulator of skeletal muscle size through expression profiling

Changes in gene expression associated with skeletal muscle atrophy due to aging are distinct from those due to disuse, suggesting that the response of old muscle to inactivity may be altered. The goal of this study was to identify changes in muscle gene expression that may contribute to loss of adaptability of old muscle. Muscle atrophy was induced in young adult (6-mo) and old (32-mo) male Brown Norway/F344 rats by 2 wk of hindlimb suspension (HS), and soleus muscles were analyzed by cDNA microarrays. Overall, similar changes in gene expression with HS were observed in young and old muscles for genes encoding proteins involved in protein folding (heat shock proteins), muscle structure, and contraction, extracellular matrix, and nucleic acid binding. More genes encoding transport and receptor proteins were differentially expressed in the soleus muscle from young rats, while in soleus muscle from old rats more genes that encoded ribosomal proteins were upregulated. The gene encoding the cold-shock protein RNA-binding motif protein-3 (RBM3) was induced most highly with HS in muscle from old rats, verified by real-time RT-PCR, while no difference with age was observed. The cold-inducible RNA-binding protein (Cirp) gene was also overexpressed with HS, whereas cold-shock protein Y-box-binding protein-1 was not. A time course analysis of RBM3 mRNA abundance during HS showed that upregulation occurred after apoptotic nuclei and markers of protein degradation increased. We conclude that a cold-shock response may be part of a compensatory mechanism in muscles undergoing atrophy to preserve remaining muscle mass and that RBM3 may be a therapeutic target to prevent muscle loss.     

Identification of the myelin oligodendrocyte glycoprotein as a cellular receptor for rubella virus

Rubella virus (RV) is a highly transmissible pathogenic agent that causes the disease rubella. Maternal RV infection during early pregnancy causes the death of the fetus or congenital rubella syndrome in infants. However, the cellular receptor for RV has not yet been identified. In this study, we found that the myelin oligodendrocyte glycoprotein (MOG) specifically bound to the E1 envelope glycoprotein of RV, and an antibody against MOG could block RV infection. Most importantly, we also showed that ectopic expression of MOG on the cell surface of 293T cells rendered this nonpermissive cell line permissive for RV entry and replication. Thus, this study has identified a cellular receptor for RV and suggests that blocking the MOG attachment site of RV may be a strategy for molecular intervention of RV infection.     

Osteoclast differentiation factor acts as a multifunctional regulator in murine osteoclast differentiation and function.

Osteoclast differentiation factor (ODF), a novel member of the TNF ligand family, is expressed as a membrane-associated protein by osteoblasts/stromal cells. The soluble form of ODF (sODF) induces the differentiation of osteoclast precursors into osteoclasts in the presence of M-CSF. Here, the effects of sODF on the survival, multinucleation, and pit-forming activity of murine osteoclasts were examined in comparison with those of M-CSF and IL-1. Osteoclast-like cells (OCLs) formed in cocultures of murine osteoblasts and bone marrow cells expressed mRNA of RANK (receptor activator of NF-kappaB), a receptor of ODF. The survival of OCLs was enhanced by the addition of each of sODF, M-CSF, and IL-1. sODF, as well as IL-1, activated NF-kappaB and c-Jun N-terminal protein kinase (JNK) in OCLs. Like M-CSF and IL-1, sODF stimulated the survival and multinucleation of prefusion osteoclasts (pOCs) isolated from the coculture. When pOCs were cultured on dentine slices, resorption pits were formed on the slices in the presence of either sODF or IL-1 but not in that of M-CSF. A soluble form of RANK as well as osteoprotegerin/osteoclastogenesis inhibitory factor, a decoy receptor of ODF, blocked OCL formation and prevented the survival, multinucleation, and pit-forming activity of pOCs induced by sODF. These results suggest that ODF regulates not only osteoclast differentiation but also osteoclast function in mice through the receptor RANK.     

LINGO-1, a transmembrane signaling protein, inhibits oligodendrocyte differentiation and myelination through intercellular self-interactions

Overcoming remyelination failure is a major goal of new therapies for demyelinating diseases like multiple sclerosis. LINGO-1, a key negative regulator of myelination, is a transmembrane signaling protein expressed in both neurons and oligodendrocytes. In neurons, LINGO-1 is an integral component of the Nogo receptor complex, which inhibits axonal growth via RhoA. Because the only ligand-binding subunit of this complex, the Nogo receptor, is absent in oligodendrocytes, the extracellular signals that inhibit myelination through a LINGO-1-mediated mechanism are unknown. Here we show that LINGO-1 inhibits oligodendrocyte terminal differentiation through intercellular interactions and is capable of a self-association in trans. Consistent with previous reports, overexpression of full-length LINGO-1 inhibited differentiation of oligodendrocyte precursor cells (OPCs). Unexpectedly, treatment with a soluble recombinant LINGO-1 ectodomain also had an inhibitory effect on OPCs and decreased myelinated axonal segments in cocultures with neurons from dorsal root ganglia. We demonstrated LINGO-1-mediated inhibition of OPCs through intercellular signaling by using a surface-bound LINGO-1 construct expressed ectopically in astrocytes. Further investigation showed that the soluble LINGO-1 ectodomain can interact with itself in trans by binding to CHO cells expressing full-length LINGO-1. Finally, we observed that soluble LINGO-1 could activate RhoA in OPCs. We propose that LINGO-1 acts as both a ligand and a receptor and that the mechanism by which it negatively regulates OPC differentiation and myelination is mediated by a homophilic intercellular interaction. Disruption of this protein-protein interaction could lead to a decrease of LINGO-1 inhibition and an increase in myelination.