Molecular systems biology in drug development.

Molecular systems biology seeks to explain the behavior of complex cellular systems through a multicomponent analysis. We illustrate this approach and its relevance to drug development by reviewing two examples of the interplay between cellular processes and drugs: the internalization and recycling of oncogenic receptors, their ligands and therapeutic antibodies; and strategies for discovering drugs that affect intracellular protein kinase pathways.

Covalent modification as a strategy to block protein-protein interactions with small-molecule drugs.

It is generally difficult to block protein-protein interactions with small-molecule drugs. A novel pharmaceutical development strategy to block protein interactions is emerging: targeted covalent modification to sterically block interactions. By this approach, compounds first interact non-covalently with a specific target protein. This interaction juxtaposes a weakly reactive group of the drug with a target amino acid sidechain, which then react by virtue of their high local concentration.

Desmoid tumour. The risk of recurrent or new disease with subsequent pregnancy: a case report.

Desmoid tumours are rare, benign tumours arising from fibrous tissue in muscle fascia or aponeurosis. They are most common in women of child-bearing age and most often appear during or after pregnancy in this age group. The recommended treatment is wide surgical excision, if possible, but unresectable tumours may be treated with radiotherapy, anticancer drugs, nonsteroidal anti-inflammatory agents or antiestrogenic compounds. The recurrence rate is high and seems to be related to the achievement of resection margins free of tumour. The literature is not specific about how to counsel women who have had a desmoid tumour and subsequently wish to have a child. Patients should be advised that these tumours may be estrogen sensitive but subsequent pregnancy is not necessarily a risk factor for recurrence or development of new disease.

Phyllodes tumour in pregnancy: a case report.

Phyllodes tumour (cystosarcoma phyllodes) is a rare breast tumour that grows rapidly and to a relatively large size, especially during pregnancy. These tumours may be classified as benign, borderline or malignant. They have a high incidence of local recurrence but little tendency to metastasize to distant organs. The question of whether the tumour is hormone dependent remains unresolved. This report describes the case of a patient who had a phyllodes tumour that first became apparent in her 31st week of pregnancy. After enucleation and subsequent wide excision she remained tumour free through a second pregnancy. Although the follow-up period is short, it appears that subsequent pregnancy is not necessarily associated with recurrent or new disease for patients who have had their initial tumour completely excised. The goal for the management of these tumours is complete surgical excision.

FP-21399 blocks HIV envelope protein-mediated membrane fusion and concentrates in lymph nodes.

The identification of fusin and other chemokine receptors as coreceptors for HIV-1 has renewed the interest in agents that may prevent viral entry. Polyanionic compounds such as dextran sulfate, curdian sulfate, and suramin act on the V3 loop of the viral envelope and may prevent its interaction with fusin. These agents show activity against a wide range of HIV-1 strains, but have undesirable circulating half-life, bioavailability, and toxicity. We have developed a small molecule inhibitor of HIV-1 that has several advantages over these other agents. FP-21399 is a novel compound of the bis(disulfonaphthalene) dimethoxybenzene class that blocks entry of HIV into CD4+ cells and blocks fusion of infected and noninfected CD4+ cells. This compound only weakly inhibits binding of CD4 and gp120, at concentrations much greater than are required to block viral entry. Furthermore, FP-21399 can block the interaction between gp120 and antibodies directed against the V3 loop, but does not block binding of antibodies directed against the V4 loop. Animal studies demonstrate that FP-21399 is concentrated in lymph nodes, making it a promising compound for anti-HIV therapy. In SCID mice reconstituted with human immune cells, maintenance of HIV-1 infection was blocked by a 5-day treatment with low doses of FP-21399, suggesting that lymph node accumulation may contribute to antiviral activity. Finally, attempts to generate drug-resistant virus in cell culture resulted in only weakly resistant variants with IC90 values that are much lower than concentrations of FP-21399 found in lymph nodes.

Establishment and cost analysis of an office surgical suite.

The objective of this study was to show that minor operative procedures done in a nonhospital setting can be provided more efficiently than those done in hospital and are agreeable to both patient and surgeon. A description of the facility, equipment required and types of procedures that can be performed provides a guide for other surgeons who may wish to establish an office surgical suite. The senior author's experience from 1993 to 1995 is described. Costs were compared on a procedure basis from financial data obtained from the practice and from a local 400-bed community hospital. Experience shows that patients are receptive to undergoing minor procedures outside the traditional hospital setting. An office surgical suite allows the surgeon greater flexibility in work scheduling, thereby improving productivity. The cost per case appears to be less in the office than in the hospital for the particular costs identified. The current method of funding minor surgical procedures provides an incentive to the surgeon to perform these procedures in hospital, because the individual practitioner is not responsible for any operating expenses. Thus, if costs are to be reduced and quality maintained, funding mechanisms must be reformed to allow less costly service to evolve.

Activation of the mec-3 promoter in two classes of stereotyped lineages in Caenorhabditis elegans.

The mec-3 gene of Caenorhabditis elegans encodes a homeodomain protein and is expressed in one of two cells upon asymmetric cell division. As a result of asymmetric mec-3 expression, the two sister cells express different fates, so mec-3 is a likely target for the machinery that mediates asymmetric cell division. The unc-86 gene encodes a homeodomain protein of the POU family, which activates mec-3 by binding to its promoter. The ten mec-3-expressing cells are a subset of the anterior daughters of UNC-86-containing cells. Posterior daughters of UNC-86-containing cells do not express mec-3, even though the UNC-86 protein is distributed into both daughter cells. Lineages that express the unc-86 and mec-3 genes can be grouped into two types: in Type I lineages, UNC-86 protein is first made in the immediate parent of the terminal mec-3-expressing cell, while in Type II lineages, UNC-86 is first made in the grandparent of the terminal mec-3-expressing cell. The purpose of experiments presented here is to understand the relationship between the mec-3 expression patterns in each type of lineage, and to determine the fundamental activity pattern of the mec-3 promoter. We find that in the Type I V5.pa lineage, mec-3-lacZ is first synthesized in the terminal PVDR neuron, one cell division after unc-86 is expressed. mec-3 expression in PVDR can occur by transcriptional regulation alone; segregation of the mec-3 RNA or protein is not required to explain the asymmetric expression of mec-3. In the Type II Q lineage, the mec-3 promoter activity can be detected in the immediate anterior daughter of the first unc-86-expressing cell, but when this cell divides, mec-3 is expressed in only one of its daughters at later times. It seems likely that, in the short-lived immediate anterior daughter cell in Type II lineages, mec-3 product does not accumulate to levels that can influence subsequent events. Our results suggest that the mec-3 promoter is activated in all anterior daughters of unc-86-expressing cells.

Promoter sequences for the establishment of mec-3 expression in the nematode Caenorhabditis elegans.

In certain stereotyped lineages of Caenorhabditis elegans, the mec-3 gene is transcribed in neurons that are anterior daughters of cells containing the UNC-86 protein. UNC-86 binds to the mec-3 promoter and is necessary for transcription activation, but this protein is present in many cells that do not transcribe mec-3, including the posterior sister and parent cells of the mec-3 expressing neurons. To understand how the mec-3 promoter directs transcription in only a subset of cells that contain UNC-86, we have compared sequences within the promoter that are bound by UNC-86 in vitro with sequences that are necessary for early transcription of mec-3 in vivo. We find that upstream of the mec-3 start codon are two blocks of sequence that are each sufficient to generate the cellular pattern of mec-3 transcription. The proximal sequence includes three previously identified short regions that have been conserved in nematode evolution and each contains one high-affinity UNC-86 binding site. The recognition consensus sequence for UNC-86 is CATnnnT/AAAT, which is identical to the recognition sequence for the UNC-86-related mammalian transcription factor Brn-3. Adjacent to the UNC-86 recognition site is an additional sequence that is important for establishment of mec-3 expression and is presumably recognized by an unidentified transcription factor.

Suppressors of the unc-73 gene of Caenorhabditis elegans.

The unc-73 gene of Caenorhabditis elegans is necessary for proper axon guidance. Animals mutant in this gene are severely uncoordinated and also exhibit defects in cell migration and cell lineages. We have isolated coordinated revertants of unc-73 (e936). These fall into three classes: intragenic revertants, extragenic dominant suppressors (sup-39), and a single apparently intragenic mutation that is a dominant suppressor with a linked recessive lethal phenotype. sup-39 mutations cause early embryonic lethality, but escapers have a wild-type movement phenotype as larvae and adults. Gonads of sup-39 mutant animals show a novel defect: normal gonads have a single row of oocytes, but sup-39 gonads often have two rows of oocytes. This result suggests that the mutant gonad is defective in choosing on its surface only a single site form which nuclei will emerge to form oocytes. These results are interpreted in terms of an effect of unc-73 on determination of cell polarity.

The mechanism of bacterial asymmetric cell division.

Asymmetric cell division generates two cells that contain different regulatory proteins and express different fates. In an example of asymmetric cell division from B. subtilis, a site on the membrane of the dividing cell is chosen to establish the initial asymmetry. Recent results show that a key regulatory protein, SpoIIE, is localized to one side of a sporulating B. subtilis cell, and subsequently functions in an asymmetric manner. SpoIIE is a phosphatase at the beginning of a regulatory cascade that leads to activation of a cell fate-determining transcription factor in only one daughter cell.

Cell polarity and the mechanism of asymmetric cell division.

During development, one mechanism for generating different cell types is asymmetric cell division, by which a cell divides and contributes different factors to each of its daughter cells. Asymmetric cell division occurs throughout the eukaryotic kingdom, from yeast to humans. Many asymmetric cell divisions occur in a defined orientation. This implies a cellular mechanism for sensing direction, which must ultimately lead to differences in gene expression between two daughter cells. In this review, we describe two classes of molecules: regulatory factors that are differentially expressed upon asymmetric cell division, and components of a signal transduction pathway that may define cell polarity. The lin-11 and mec-3 genes of C. elegans, the Isl-1 gene of mammals and the HO gene of yeast, encode regulatory factors that determine cell type of one daughter after asymmetric cell division. The CDC24 and CDC42 genes of yeast affect both bud positioning and orientation of mating projections, and thus may define a general cellular polarity. We speculate that molecules such as Cdc24 and Cdc42 may regulate expression of genes such as lin-11, mec-3, Isl-1 and HO upon asymmetric cell division.

Regulation of anterior cell-specific mec-3 expression during asymmetric cell division in C. elegans.

The homeobox-containing mec-3 gene of C. elegans is expressed in 10 mechanosensory neurons and is necessary for these cells to acquire their fate. All the mec-3-expressing cells are anterior daughters from an asymmetric cell division. In this paper, we examine the expression of a mec-3--lacZ fusion in the presence of mutations that may disrupt asymmetric cell division or anterior-posterior positional information, as well as mutations that may specifically alter mec-3 expression. A mutation in lin-17 causes production of additional mec-3-expressing cells and can have its effect on the cell division that produces a mec-3-expressing cell. In a lin-5 mutant, in which postembryonic blast cells do not complete cell division and become polyploid, blast cells that would give rise to mec-3-expressing daughters instead express mec-3 themselves. In a lin-12 glp-1 double mutant, which is disrupted for many cell interactions in which two cells compete for the same fate, mec-3 expression is unaffected. These results are consistent with a model for asymmetric cell division in which the mec-3-expressing cell and its sister are different immediately upon cell division, rather than acquiring differences through later interaction with each other or their surroundings. lin-17 mutant animals also show defects in the position of the PVM cell and the PLM axons. Animals mutant in unc-73 and unc-40, known to have axon outgrowth defects, also show errors in PVM position and a low frequency of additional mec-3-expressing cells, as well as occasional secondary vulval protrusions, a common phenotype of lin-17 animals. Many other mutations have either no effect on mec-3 expression or an effect that can be largely predicted from previously known phenotypes: these include mab-5, mig-1, unc-53, egl-5, lin-32, and egl-27. unc-11 shows an unexpected and specific defect in mec-3 expression in the PVD neurons, but not in the other mec-3-expressing cells. Two mutations that suppress the egg-laying defect of unc-86 have no effect on the mec-3 expression defect in an unc-86 mutant.

The mec-7 beta-tubulin gene of Caenorhabditis elegans is expressed primarily in the touch receptor neurons.

Mutants of the mec-7 beta-tubulin gene of Caenorhabditis elegans lack the large diameter 15-protofilament microtubules normally found only in the set of six touch receptor neurons. Both a mec-7-lacZ reporter gene and affinity-purified anti-mec-7 antibodies were used to show that mec-7 is expressed primarily in the touch neurons. These data are consistent with a possible instructive role for the mec-7 tubulin in determining microtubule protofilament number. The antibodies and the mec-7-lacZ transgene were also used to examine mec-7 expression in mutants affecting the generation, differentiation or maintenance of the touch neurons. Decreased expression was observed in mutants of unc-86 and mec-3, genes that encode transcription factors essential for touch receptor neuron generation and differentiation, respectively.

The mec-3 gene contains cis-acting elements mediating positive and negative regulation in cells produced by asymmetric cell division in Caenorhabditis elegans.

The homeo box-containing genes mec-3 and unc-86 are necessary to specify the fate of a defined set of mechanoreceptors in Caenorhabditis elegans. Previous experiments have shown that mec-3 expression can be divided into two phases: initial synthesis mediated in part by unc-86, and continued synthesis that requires mec-3 itself. We now identify sequences that have been conserved during Caenorhabditis evolution and are necessary for establishment, maintenance, and repression of mec-3 expression. Upstream of the start codon for the mec-3-coding sequence are four segments (regions I-IV) of 71, 29, 28, and 24 bp, which are almost identical between C. elegans and Caenorhabditis vulgarensis. Region I is the only conserved sequence that effects establishment of mec-3 synthesis. Maintenance of mec-3 expression is mediated primarily by region II. Repression appears to be controlled by several segments: Mutation of region III, region IV, and parts of region I in a mec-3-lacZ fusion results in beta-galactosidase expression in some non-mec-3-expressing sisters of mec-3-positive cells. These results indicate that the mec-3 5' region contains target sequences that mediate a genetic switch between alternative fates expressed by sister cells in a stereotyped cell lineage.

The mec-3 gene of Caenorhabditis elegans requires its own product for maintained expression and is expressed in three neuronal cell types.

The homeo-box-containing gene mec-3 of the nematode Caenorhabditis elegans, is expressed in several sensory neurons, as assayed by expression of a mec-3-lacZ fusion. These cells are the touch receptors, which mediate the response to gentle touch, and the FLP and PVD neurons. PVD mediates a response to harsh mechanical stimuli, and FLP has an ultrastructure suggestive of a mechanoreceptor, but its function is unknown. mec-3 is necessary for the differentiation of the touch receptors, because in mec-3 mutants, the touch receptors do not function and have none of their distinguishing features. mec-3 is also needed for PVD function: The PVD neurons no longer mediate a response to harsh mechanical stimuli in the mutants. The expression of the mec-3-lacZ fusion, and presumably mec-3 itself, is altered by mutations in several genes originally identified by their effects on touch cell development. unc-86, another homeo-box-containing gene, is necessary for all mec-3-lacZ expression, but also affects several other lineages and cells in which mec-3 is not expressed. mec-3 activity appears to be required for maintained expression of the mec-3-lacZ fusion in all cells in which it is expressed. In a mec-17 mutant, mec-3-lacZ expression is not maintained in the touch receptors, but is not affected in the FLP and PVD neurons. These findings suggest that combinatorial mechanisms of gene regulation control both the expression of mec-3 itself and its action in promoting the terminal differentiation of various cell types.

mec-3, a homeobox-containing gene that specifies differentiation of the touch receptor neurons in C. elegans.

The mec-3 gene is essential for proper differentiation of the set of six touch receptor neurons in C. elegans. In mutants lacking mec-3 activity, the touch receptors express none of their unique differentiated features and appear to be transformed into other types of neurons. We cloned the mec-3 gene by transposon tagging and showed that a mec-3 mutant can be rescued by germ line transformation using a 5.6 kb genomic DNA fragment. In a strain in which transforming mec-3 DNA is present in about 50 copies per haploid genome, additional cells express a mec-3-dependent phenotype. The putative coding sequence of mec-3 contains a homeobox, suggesting that the mec-3 protein specifies the expression of touch cell differentiation by binding to DNA and regulating transcription of genes that encode the differentiated features of these cells.

Transposition of plasmid-borne Tn10 elements does not exhibit simple length-dependence.

The transposition frequencies of Tn10 elements from the bacterial chromosome to an F epitome decrease 40% for every kilobase increase in transposon length. The basis for this relationship is not known. We have now examined complemented transposition of defective Tn10 elements off small multicopy plasmids. We find that length dependence in this situation is either reduced or absent, depending on the specific class of transposition events involved. These observations can be interpreted as evidence against the model that chromosomal length dependence occurs because of decay of a transposition-associated replicative complex. This interpretation is consistent with unrelated experiments suggesting that Tn10 transposition is normally nonreplicative. Alternative explanations of length dependence phenomena are discussed.

New Tn10 derivatives for transposon mutagenesis and for construction of lacZ operon fusions by transposition.

We describe below several new variants of the tetracycline-resistance transposon Tn10 which are more useful than the wild-type transposon for many types of genetic and physical analysis of bacteria. These derivatives have one or more of the following new properties: (i) new drug resistance markers; (ii) high transposition frequencies; (iii) removal of the transposase gene to a position outside of the transposing segment; (iv) internal deletions which eliminate the ability of Tn10 to make adjacent deletion/inversions; or (v) addition of a trp-lac operon fusion segment just inside one terminus such that insertion can automatically generate a transcriptional fusion to the interrupted operon. Phage and plasmid vehicles carrying these new elements are described.