MINERVA: a multi-modality plugin-based radiation therapy treatment planning system.

Researchers at the INEEL, MSU, LLNL and UCD have undertaken development of MINERVA, a patient-centric, multi-modal, radiation treatment planning system, which can be used for planning and analysing several radiotherapy modalities, either singly or combined, using common treatment planning tools. It employs an integrated, lightweight plugin architecture to accommodate multi-modal treatment planning using standard interface components. The design also facilitates the future integration of improved planning technologies. The code is being developed with the Java programming language for interoperability. The MINERVA design includes the image processing, model definition and data analysis modules with a central module to coordinate communication and data transfer. Dose calculation is performed by source and transport plugin modules, which communicate either directly through the database or through MINERVA's openly published, extensible markup language (XML)-based application programmer's interface (API). All internal data are managed by a database management system and can be exported to other applications or new installations through the API data formats. A full computation path has been established for molecular-targeted radiotherapy treatment planning, with additional treatment modalities presently under development.

Defective TNF-alpha-induced apoptosis in STAT1-null cells due to low constitutive levels of caspases.

Signal transducers and activators of transcription (STATs) enhance transcription of specific genes in response to cytokines and growth factors. STAT1 is also required for efficient constitutive expression of the caspases Ice, Cpp32, and Ich-1 in human fibroblasts. As a consequence, STAT1-null cells are resistant to apoptosis by tumor necrosis factor alpha (TNF-alpha). Reintroduction of STAT1alpha restored both TNF-alpha-induced apoptosis and the expression of Ice, Cpp32, and Ich-1. Variant STAT1 proteins carrying point mutations that inactivate domains required for STAT dimer formation nevertheless restored protease expression and sensitivity to apoptosis, indicating that the functions of STAT1 required for these activities are different from those that mediate induced gene expression.

Both loss-of-function and gain-of-function mutations in snf define a role for snRNP proteins in regulating Sex-lethal pre-mRNA splicing in Drosophila development.

The Drosophila snf gene encodes a protein with functional homology to the mammalian U1A and U2B" snRNP proteins. Studies, based on the analysis of three viable alleles, have suggested a role for snf in establishing the female-specific splicing pattern of the sex determination switch gene, sex-lethal. Here, we show that the non-sex-specific lethal null allele is required for female sex determination, arguing against the formal possibility that the viable alleles disrupt a function unrelated to snf's wild-type function. Moreover, we find snf is required for normal cell growth and/or survival, as expected for a protein involved in a cell-vital process such as RNA splicing. We also show that of the three viable alleles only one, snfJA2, is a partial loss-of-function mutation. The other two viable alleles, snf1621 and snfe8H, encode antimorphic proteins. We find the antimorphic proteins are mislocalized and correlate their mislocalization with their molecular lesions and mutant phenotypes. Finally, we provide genetic evidence that the antimorphic alleles interfere with the autoregulatory splicing function of the Sex-lethal protein. Based on these studies we suggest a model in which the snRNP protein, Snf, functions with Sex-lethal to block recognition of the regulated male-specific exon.

Roles of JAKs in activation of STATs and stimulation of c-fos gene expression by epidermal growth factor.

The tyrosine kinase JAK1 and the transcription factors STAT1 and STAT3 are phosphorylated in response to epidermal growth factor (EGF) and other growth factors. We have used EGF receptor-transfected cell lines defective in individual JAKs to assess the roles of these kinases in STAT activation and signal transduction in response to EGF. Although JAK1 is phosphorylated in response to EGF, it is not required for STAT activation or for induction of the c-fos gene. STAT activation in JAK2- and TYK2-defective cells is also normal, and the tyrosine phosphorylation of these two kinases does not increase upon EGF stimulation in wild-type or JAK1-negative cells. In cells transfected with a kinase-negative mutant EGF receptor, there is no STAT activation in response to EGF and c-fos is not induced, showing that the kinase activity of the receptor is required, directly or indirectly, for these two responses. The data do not support a role for any of the three JAK family members tested in STAT activation and are consistent with a JAK-independent pathway in which the intrinsic kinase domain of the EGF receptor is crucial. Furthermore, data from transient transfection experiments in HeLa cells, using c-fos promoters lacking the STAT regulatory element c-sis-inducible element, indicate that this element may play only a minor role in the induction of c-fos by EGF in these cells.

The Drosophila sex determination gene snf encodes a nuclear protein with sequence and functional similarity to the mammalian U1A snRNP protein.

Alternative splicing controls the expression of many genes, including the Drosophila sex determination gene Sex-lethal. Previous studies have suggested that snf plays a role in regulating Sex-lethal splicing. Here, we demonstrate that snf is an integral component of the machinery required for splice site recognition. We have cloned snf and found that it has sequence homology to the mammalian U1A and U2B" snRNP proteins. Moreover, we establish that snf encodes a Drosophila protein shown previously to have functional similarity to U1A. Finally, with the isolation and analysis of a null mutation, we demonstrate that snf is an essential gene. These studies provide the first demonstration, in a multicellular organism, that mutations in a U1 snRNP protein alter splicing in vivo.

The Drosophila maternal effect locus deadhead encodes a thioredoxin homolog required for female meiosis and early embryonic development.

This study describes the identification, function and molecular characterization of deadhead, a Drosophila thioredoxin homolog. Although in vitro studies have shown that thioredoxin can post-translationally regulate the activity of many different proteins, we find that this homolog is not essential for viability. The phenotypic analysis of two different mutations which eliminate function suggests that dhd is essential for female meiosis. The majority of eggs laid by females homozygous for null mutations are fertilized but fail to complete meiosis. A small number of escaper embryos initiate development and display a range of phenotypes suggesting functions in both preblastoderm mitosis and head development. Our analysis of deadhead's RNA expression pattern is consistent with its maternal effect function: the RNA is predominately expressed in the nurse cells of the ovary, is maternally deposited into the egg, but does not appear to be zygotically expressed during embryogenesis. Thus both our genetic and molecular data are consistent with a function during meiosis and preblastoderm mitosis. Whether the head defect indicates an additional function or is an indirect consequence of earlier defects remains to be determined.

A complete description of the EGF-receptor exon structure: implication in oncogenic activation and domain evolution.

In this paper, we report that the chicken Epidermal Growth Factor Receptor (EGF-R), encoded by the proto-oncogene c-erbB, is comprised of 28 exons and spans over 75 Kb. The four previously identified domains which make up the extracellular ligand binding region of the receptor are coded for by two copies of a 300 amino acid repeat. We have demonstrated that the 3' end of each repeat coincides with the 3' end of the last exon making up the repeat. This alignment suggests that an exon-duplication may have occurred in the ligand-binding region of the gene. The transmembrane domain is encoded within a single exon and the exon boundaries of the catalytic domain closely match those defined by structural homology with other kinases. Along with the 54 chicken splice sites, the region 5' to the first exon was also sequenced. The proposed promoter region is greater than 70% GC, contains five repeats of the consensus Sp1 binding sequence and does not have a CCATT or TATA box. In addition to the presence of these characteristic housekeeping features, expression analysis confirms the promoter activity of this region and four sets of TCC repeats similar to those found in the human EGF-R promoter have been identified. To our knowledge this represents the first complete description of the exon-intron structure of the EGF-receptor family. The elucidation of the EGF-R exon structure provides insight into the domain evolution of the receptor-kinases and the mechanisms for the oncogenic conversion of EGF-R in erythroleukemias and glioblastomas.

An alternatively processed mRNA from the avian c-erbB gene encodes a soluble, truncated form of the receptor that can block ligand-dependent transformation.

At least four major transcripts are produced by the avian c-erbB/epidermal growth factor receptor gene. cDNAs corresponding to the smallest one, a 2.6-kb transcript, were isolated from an adult chicken liver cDNA library. Sequence analysis revealed that the 3' end of one cDNA clone diverged from the known sequence of the extracellular ligand-binding domain (LBD) of the full-length receptor. A genomic DNA subfragment that contained this unique 3' divergent end was isolated. Sequence analysis of this genomic DNA fragment revealed that the 2.6-kb c-erbB transcript is produced by alternative processing. Translation of this 2.6-kb transcript would produce a secreted, truncated receptor molecule which contains the amino-terminal three-fourths of the extracellular LBD of the native receptor. COS1 cells and primary chicken embryo fibroblast cells were transfected with expression vectors that contained the 2.6-kb c-erbB cDNA. Conditioned medium from these transfected cells contained a 70-kDa protein that was specifically immunoprecipitated by a polyclonal antiserum directed against the LBD of the avian c-erbB gene product. The 70-kDa truncated receptor could be coimmunoprecipitated from conditioned medium of transfected COS1 cells that was supplemented with recombinant human transforming growth factor alpha (TGF alpha) by a monoclonal antibody against human TGF alpha. Additionally, transfected chicken embryo fibroblast cells that overexpressed the 70-kDa truncated receptor were blocked in their ability to form TGF alpha-dependent colonies in soft agar. These data suggest that the secreted, truncated receptor encoded by the 2.6-kb c-erbB transcript can bind to TGF alpha and may play an important growth-regulatory function in vitro.

EGF-R as a hemopoietic growth factor receptor: the c-erbB product is present in chicken erythrocytic progenitors and controls their self-renewal.

c-erbB, encoding the EGF receptor (EGF-R), was originally identified as the cellular homolog of a chicken leukemia oncogene. In humans, EGF-R is distributed widely except in hemopoietic tissues, and its amplification is associated with epidermal and glial malignancies. Here we show that c-erbB is present in normal chicken erythrocytic progenitors and transmits the mitogenic signal induced by TGF alpha. Cells that contain high affinity EGF-R are at approximately the BFU-E stage, and their long-term renewal can be induced by TGF alpha. Upon addition of insulin and erythropoietin, they can be induced to terminally differentiate into red cells. We previously demonstrated that v-erbA blocks differentiation of chicken erythrocytic progenitors but does not abrogate their growth factor dependence for proliferation. These data indicate that proliferation and differentiation are not necessarily coupled in these cells. They also demonstrate a direct role of c-erbB in the control of self-renewal of normal chicken erythrocytic progenitors and could account for the predominant leukemogenic potential of the chicken erbB gene.

Native avian c-erbB gene expresses a secreted protein product corresponding to the ligand-binding domain of the receptor.

A primer-directed cDNA library was used to obtain cDNA clones corresponding to the 5' end (i.e., the ligand-binding domain) of the avian c-erbB gene. Bacterial c-erbB fusion proteins were synthesized and used to obtain polyclonal antisera specific for the ligand-binding domain of the avian receptor. These antisera and antisera specific for the carboxyl terminal domain of the chicken c-erbB gene product have been used to study the native protein products of the c-erbB locus in primary cell cultures by in vivo labeling and immunoprecipitation. Our studies reveal that three c-erbB gene products of Mr 300,000, Mr 170,000, and Mr 95,000 are synthesized in uninfected chicken embryo fibroblasts. Only the Mr 300,000 and Mr 170,000 species can be precipitated by using antisera specific for the cytoplasmic domain of the c-erbB product. The 95,000 species is not recognized by the antiserum directed against the carboxyl-terminal domain of c-erbB and is specifically released into the culture medium. Northern transfer studies reveal a lower molecular weight transcript of approximately 2.6 kilobases that selectively hybridizes to the ligand-binding domain of the avian c-erbB gene product but does not hybridize with probes specific for the cytoplasmic kinase domain of c-erbB. An additional cDNA clone corresponding to this transcript has been isolated, and its sequence suggests it may arise via alternative processing. Together, these data suggest that a truncated form of this growth factor receptor--i.e., a Mr 95,000 species--is synthesized from a low molecular weight c-erbB transcript that exclusively encodes the ligand-binding domain of the receptor. Secretion of truncated growth factor receptors has been reported recently in several systems, and our results are discussed in the light of these findings.

Proviral insertional activation of c-erbB: differential processing of the protein products arising from two alternate transcripts.

Proviral insertional activation of c-erbB results in the expression of two alternate transcripts (ENV+ and ENV-). We used cDNA clones representing the two alternate transcripts to generate stably transformed quail fibroblast cell lines which express the products of these transcripts independently. Analysis of the co- and posttranslational processing of the insertionally activated c-erbB products expressed in these cell lines revealed that the protein products of the ENV+ and ENV- transcripts were processed differently. The ENV+ transcript produced a primary translation product which was rapidly cotranslationally cleaved near the amino terminus to form a 79,000-Mr product. This protein product was efficiently converted to a higher-molecular-weight form, of between 82,000 and 88,000 (gp82-88), which was terminally glycosylated and expressed on the cell surface. A small portion of the ENV+ primary translation product underwent a second proteolytic cleavage to generate an unglycosylated 53,000-Mr species. In contrast, the primary translation product of the ENV- transcript, p80, was not proteolytically processed; this precursor form was rapidly converted to two discrete glycosylation intermediates, gp82 and go84. Only a small portion (less than 10%) of the total ENV- insertionally activated c-erbB product was slowly converted to the terminally glycosylated cell surface form, gp85-88. The processing differences that distinguished the ENV+ and ENV- products were similar to processing differences that we observed in parallel studies on the viral erbB products of the avian erythroblastosis viruses AEV-H and AEV-R, respectively. Since all four erbB protein products shared the same number, position, and sequence context of potential N-linked glycosylation sites, yet differed in the extent of their carbohydrate maturation, these data suggest that the mechanisms used by these truncated receptor molecules to associate with cellular membranes may be distinct.