Previously Uncharacterized Vacuolar-type ATPase Binding Site Discovered from Structurally Similar Compounds with Distinct Mechanisms of Action

Using a comprehensive chemical genetics approach, we identified a member of the lignan natural product family, HTP-013, which exhibited significant cytotoxicity across various cancer cell lines. Correlation of compound activity across a panel of reporter gene assays suggested the vacuolar-type ATPase (v-ATPase) as a potential target for this compound. Additional cellular studies and a yeast haploinsufficiency screen strongly supported this finding. Competitive photoaffinity labeling experiments demonstrated that the ATP6V0A2 subunit of the v-ATPase complex binds directly to HTP-013, and further mutagenesis library screening identified resistance-conferring mutations in ATP6V0A2. The positions of these mutations suggest the molecule binds a novel pocket within the domain of the v-ATPase complex responsible for proton translocation. While other mechanisms of v-ATPase regulation have been described, such as dissociation of the complex or inhibition by natural products including bafilomycin A1 and concanamycin, this work provides detailed insight into a distinct binding pocket within the v-ATPase complex.

Evidence-Based and Quantitative Prioritization of Tool Compounds in Phenotypic Drug Discovery

The use of potent and selective chemical tools with well-defined targets can help elucidate biological processes driving phenotypes in phenotypic screens. However, identification of selective compounds en masse to create targeted screening sets is non-trivial. A systematic approach is needed to prioritize probes, which prevents the repeated use of published but unselective compounds. Here we performed a meta-analysis of integrated large-scale, heterogeneous bioactivity data to create an evidence-based, quantitative metric to systematically rank tool compounds for targets. Our tool score (TS) was then tested on hundreds of compounds by assessing their activity profiles in a panel of 41 cell-based pathway assays. We demonstrate that high-TS tools show more reliably selective phenotypic profiles than lower-TS compounds. Additionally we highlight frequently tested compounds that are non-selective tools and distinguish target family polypharmacology from cross-family promiscuity. TS can therefore be used to prioritize compounds from heterogeneous databases for phenotypic screening.

Yb modulates the divisions of both germline and somatic stem cells through piwi- and hh-mediated mechanisms in the Drosophila ovary

The coordinated division of distinctive types of stem cells within an organ is crucial for organogenesis and homeostasis. Here we show genetic interactions among fs(1)Yb (Yb), piwi, and hedgehog (hh) that regulate the division of both germline stem cells (GSCs) and somatic stem cells (SSCs), the two constituent stem cell populations of the Drosophila ovary. Yb is required for both GSC and SSC divisions; loss of Yb function eliminates GSCs and reduces SSC division, while Yb overexpression increases GSC number and causes SSC overproliferation. We also show that Yb acts via the piwi- and hh-mediated signaling pathways that emanate from the same signaling cells to control GSC and SSC division, respectively. hh signaling also has a minor effect in GSC division.

Somatic signaling mediated by fs(1)Yb is essential for germline stem cell maintenance during Drosophila oogenesis

Drosophila oogenesis starts when a germline stem cell divides asymmetrically to generate a daughter germline stem cell and a cystoblast that will develop into a mature egg. We show that the fs(1)Yb gene is essential for the maintenance of germline stem cells during oogenesis. We delineate fs(1)Yb within a 6.4 kb genomic region by transgenic rescue experiments. fs(1)Yb encodes a 4.1 kb RNA that is present in the third instar larval, pupal and adult stages, consistent with its role in regulating germline stem cells during oogenesis. Germline clonal analysis shows that all fs(1)Yb mutations are soma-dependent. In the adult ovary, fs(1)Yb is specifically expressed in the terminal filament cells, suggesting that fs(1)Yb acts in these signaling cells to maintain germline stem cells. fs(1)Yb encodes a novel hydrophilic protein with no potential signal peptide or transmembrane domains, suggesting that this protein is not itself a signal but a key component of the signaling machinery for germline stem cell maintenance.

DEF-1, a novel Src SH3 binding protein that promotes adipogenesis in fibroblastic cell lines

The Src homology 3 (SH3) motif is found in numerous signal transduction proteins involved in cellular growth and differentiation. We have purified and cloned a novel protein, DEF-1 (differentiation-enhancing factor), from bovine brain by using a Src SH3 affinity column. Ectopic expression of DEF-1 in fibroblasts resulted in the differentiation of a significant fraction of the culture into adipocytes. This phenotype appears to be related to the induction of the transcription factor peroxisome proliferator-activated receptor gamma (PPARgamma), since DEF-1 NIH 3T3 cells demonstrated augmented levels of PPARgamma mRNA and, when treated with activating PPARgamma ligands, efficient induction of differentiation. Further evidence for a role for DEF-1 in adipogenesis was provided by heightened expression of DEF-1 mRNA in adipose tissue isolated from obese and diabetes mice compared to that in tissue isolated from wild-type mice. However, DEF-1 mRNA was detected in multiple tissues, suggesting that the signal transduction pathway(s) in which DEF-1 is involved is not limited to adipogenesis. These results suggest that DEF-1 is an important component of a signal transduction process that is involved in the differentiation of fibroblasts and possibly of other types of cells.

Differentiation and reversal of malignant changes in colon cancer through PPARgamma

PPARgamma is a nuclear receptor that has a dominant regulatory role in differentiation of cells of the adipose lineage, and has recently been shown to be expressed in the colon. We show here that PPARgamma is expressed at high levels in both well- and poorly-differentiated adenocarcinomas, in normal colonic mucosa and in human colon cancer cell lines. Ligand activation of this receptor in colon cancer cells causes a considerable reduction in linear and clonogenic growth, increased expression of carcinoembryonic antigen and the reversal of many gene expression events specifically associated with colon cancer. Transplantable tumors derived from human colon cancer cells show a significant reduction of growth when mice are treated with troglitazone, a PPARgamma ligand. These results indicate that the growth and differentiation of colon cancer cells can be modulated through PPARgamma.

Increased bone mineral content of preterm infants fed with a nutrient enriched formula after discharge from hospital

Bone disease with persistent reduced bone mineralisation is common in premature infants. To test the hypothesis that enhancement of nutritional intake after discharge from hospital improves bone mineralisation, 31 formula fed preterm infants were randomly assigned to receive standard or multinutrient enriched milk from the time of discharge. The calcium and phosphorus contents of the enriched milk were 70 and 35 mg/100 ml v 35 and 29 mg/100 ml for the standard formula. Bone mineral content was measured before discharge from hospital in 21 of the infants; there was no difference in the bone mineral content between the groups at that time (35 mg/cm for the two groups). There was a significant increase in bone mineral content for those infants receiving the enriched v standard formula at 3 and 9 months corrected postnatal age: at 3 months the bone mineral content was 83 v 63 mg/cm and at 9 months 115 v 95 mg/cm. The difference between the groups was thus maintained although not increased at a corrected age of 9 months, when the bone mineral content of infants fed the enriched but not the standard formula was no longer significantly different from that of normal infants after adjusting for body size. The difference was not explained by the larger body size in infants fed the enriched formula. The results suggest that the use of a special nutrient enriched postdischarge formula has a significant positive effect on bone growth and mineralisation during a period of rapid skeletal development.

Randomised trial of nutrition for preterm infants after discharge

In a randomised double blind trial, the effect on growth and clinical status of a nutrient enriched 'post-discharge' milk formula versus a standard term formula, was compared in 32 exclusively bottle fed preterm infants. The formulas were used as the sole milk intake up to a postnatal age of 9 months. Significant increases in linear growth and weight gain were observed in the infants who received the enriched diet. There were no differences in vomiting, posseting, or bowel habit between the groups. Formula volumes ingested were similar between diet groups, indicating that the difference in formula composition did not affect the infants' regulation of intake. These preliminary data suggest that there is a role for specially designed formulas for preterm infants after discharge from hospital.

A colony-stimulating factor 1 (CSF-1) receptor/platelet-derived growth factor-beta receptor gene fusion confers CSF-1 independence and tumorigenicity on a c-myc-immortalized monocyte cell line

Monocytes and macrophages express the receptor for the hematopoietic growth factor colony-stimulating factor 1 (CSF-1) and require this factor for growth in culture. A murine monocyte tumor cell line that lacks the usual requirement for CSF-1 was isolated. On the basis of the similarity of the structures of the CSF-1 and platelet-derived growth factor (PDGF) receptors and because monocytes normally secrete PDGF, we analyzed the tumor cell line for anomalous expression of the PDGF-R beta gene. Two different cDNAs that each contain sequences corresponding to the complete coding sequence of PDGF-R beta fused (in frame) to the amino-terminal half of the CSF-1 receptor were isolated. Introduction of these PDGF-R beta-related cDNAs into two partially transformed, CSF-1-dependent monocyte cell lines resulted in autonomous growth and cell transformation. These monocyte cell lines exhibit a novel form of growth factor receptor activation that can lead to oncogenic growth in collaboration with the c-myc oncogene.

Linear growth in the early neonatal period

To test the hypothesis that early linear growth is independent of changes in weight we undertook took simple anthropometry in 45 term infants daily to day 7 after birth. Linear growth proceeded rapidly and independently of changes in weight variations from the first day after birth; we suggest that this implies 'programmed' continuity of skeletal growth, possibly fuelled at the expense of other body tissues.

Paradoxical bone mineralisation in the twin to twin transfusion syndrome

We report twin preterm infants with the twin to twin transfusion syndrome, exhibiting grossly different bone densities on chest radiographs. Photonabsorptiometry showed the polycythaemic twin was osteopenic and the anaemic twin osteosclerotic; bone mineral contents were 0.028 g/cm and 0.074 g/cm respectively (normal mean (SD) 0.041 (0.006) g/cm. We speculate that alterations in macrophage derived osteoclastic activity contribute to these previously unreported findings.

Molecular cloning and sequencing of the murine c-fgr gene

The c-fgr gene is a member of the tyrosine kinase family of proto-oncogenes and is expressed exclusively in hemopoietic cells. We found that c-fgr was expressed at high levels in a limited subset of murine monocyte/macrophage tumors that were induced by the c-myc oncogene, in cells representing late stages of monocyte differentiation. A cDNA clone was isolated from a library made from a monocyte tumor cell lines using a human c-fgr and v-fgr probe. The composite nucleotide and predicted amino acid sequence of the cDNA indicates that it represents the complete coding sequence for the murine c-fgr gene. Comparison of the N-terminal human and mouse c-fgr amino acid sequences indicates regions of identity that are not homologous to other tyrosine kinases. Interestingly, these regions share a limited but significant homology to two viral proteins, adenovirus E1b and HIV nef. In addition, there are other regions of homology that are shared by several tyrosine kinases and other non-kinase proteins which may be important for subcellular localization.