Rat c-raf oncogene activation by a rearrangement that produces a fused protein

Rearrangements of NTRK1 gene in papillary thyroid carcinoma

TRK oncogenes are observed in a consistent fraction of papillary thyroid carcinoma (PTC); they arise from the fusion of the 3' terminal sequences of the NTRK1/NGF receptor gene with 5' terminal sequences of various activating genes, such as TPM3, TPR and TFG. TRK oncoproteins display constitutive tyrosine-kinase activity, leading to in vitro and in vivo transformation. In this review studies performed during the last 20 years will be summarized. The following topics will be illustrated: (a) frequency of TRK oncogenes and correlation with radiation and tumor histopathological features; (b) molecular mechanisms underlying NTRK1 oncogenic rearrangements; (c) molecular and biochemical characterization of TRK oncoproteins, and their mechanism of action; (d) role of activating sequences in the activation of TRK oncoproteins.

Spatiotemporal control of mitosis by the conserved spindle matrix protein Megator

A putative spindle matrix has been hypothesized to mediate chromosome motion, but its existence and functionality remain controversial. In this report, we show that Megator (Mtor), the Drosophilamelanogaster counterpart of the human nuclear pore complex protein translocated promoter region (Tpr), and the spindle assembly checkpoint (SAC) protein Mad2 form a conserved complex that localizes to a nuclear derived spindle matrix in living cells. Fluorescence recovery after photobleaching experiments supports that Mtor is retained around spindle microtubules, where it shows distinct dynamic properties. Mtor/Tpr promotes the recruitment of Mad2 and Mps1 but not Mad1 to unattached kinetochores (KTs), mediating normal mitotic duration and SAC response. At anaphase, Mtor plays a role in spindle elongation, thereby affecting normal chromosome movement. We propose that Mtor/Tpr functions as a spatial regulator of the SAC, which ensures the efficient recruitment of Mad2 to unattached KTs at the onset of mitosis and proper spindle maturation, whereas enrichment of Mad2 in a spindle matrix helps confine the action of a diffusible “wait anaphase” signal to the vicinity of the spindle.

Flesh and blood: The story of Vav1, a gene that signals in hematopoietic cells but can be transforming in human malignancies

Cancer results from the interaction of multiple aberrations including activation of dominant oncogenes and upregulation of signal transduction pathways. Identification of the genes involved in malignant transformation is a pre-requisite for understanding cancer and improving its diagnosis and treatment. Quite a few of the genes that have been implicated in cancer are mutant or aberrantly expressed versions of genes that are important mediators of the normal growth that occurs during development. An important example of this is Vav1, a cytoplasmic signal transducer protein initially identified as an oncogene. Physiological expression of Vav1 is restricted to the hematopoietic system, where its best-known function is as a GDP/GTP nucleotide exchange factor for Rho/Rac GTPases, an activity strictly controlled by tyrosine phosphorylation. Vav1 was shown to regulate cytoskeletal rearrangement during activation of hematopoietic cells. Vav1 can also mediate other cellular functions including activation of the JNK, ERK, Ras, NF-kB, and NFAT pathways, in addition to association with numerous adapter proteins such as Shc, NCK, SLP-76, GRB2, and Crk. Although the oncogenic form of Vav1 has not been detected in clinical human tumors, its wild-type form has recently been implicated in mammalian malignancies such as neuroblastoma, melanoma, pancreatic tumors and B-cell chronic lymphocytic leukemia. This review addresses the physiological function of wild-type Vav1, its mode of activation as an oncogene, and its emerging role as a transforming protein in human cancer.

Oncogenic rearrangements of the NTRK1/NGF receptor

The NTRK1 gene encodes the high affinity receptor for Nerve Growth Factor, and its action regulates neural development and differentiation. Deregulation of NTRK1 activity is associated with several human disorders. Loss of function mutations causes the genetic disease congenital insensitivity to pain with anhidrosis (CIPA). Constitutive activation of NTRK1 has been detected in several tumor types. An autocrine loop involving NTRK1 and NGF is associated with tumor progression in prostate carcinoma and in breast cancer. A novel alternative splicing variant with constitutive oncogenic potential has been recently described in neuroblastoma. Somatic rearrangements of NTRK1, producing chimeric oncogenes with constitutive tyrosine kinase activity, have been detected in a consistent fraction of papillary thyroid tumors. The topic of this review is a detailed analysis of the thyroid TRK oncogenes. The modalities of their activation, their mechanism of action, the contribution of activating sequences, and the molecular mechanisms underlying their generation will be discussed.

The mouse interferon-inducible gene Ifi204 product interacts with the Tpr protein, a component of the nuclear pore complex

We have used yeast two-hybrid screening to isolate cDNA-encoding proteins interacting with the protein encoded by the interferon (IFN)-inducible gene Ifi204. Four independent overlapping clones were isolated from an NIH3T3 cDNA library. The largest clone encoded a protein (1203 amino acids in length) sharing 94% identity with the C-terminal portion of the human translocated promoter region (Tpr) protein. Northern blot analysis revealed a 7.5-kilobase mRNA present in both mouse and human cell lines. In addition, in vivo interaction was demonstrated by coimmunoprecipitation experiments. Anti-Tpr polyclonal monospecific antibodies (Ab) used for immunofluorescence staining labeled the nuclear envelope (NE) in a punctate pattern characteristic of nucleoporins and also yielded staining throughout the nuclear interior. The intranuclear Tpr occurred in apparently discrete foci. When superimposed on optical sections obtained with anti-p204 Abs, these colocalized, with the sole exception of the nucleolar compartment stained by the anti-p204 Abs only. Although the specific function of Tpr is not defined, it appears to mediate p204 translocation from the cytoplasmic to the nuclear compartment following IFN treatment.

The Raf/MEK/ERK signal transduction cascade as a target for chemotherapeutic intervention in leukemia

The Raf/MEK/ERK (MAPK) signal transduction cascade is a vital mediator of a number of cellular fates including growth, proliferation and survival, among others. The focus of this review centers on the MAPK signal transduction pathway, its mechanisms of activation, downstream mediators of signaling, and the transcription factors that ultimately alter gene expression. Furthermore, negative regulators of this cascade, including phosphatases, are discussed with an emphasis placed upon chemotherapeutic intervention at various points along the pathway. In addition, mounting evidence suggests that the PI3K/Akt pathway may play a role in the effects elicited via MAPK signaling; as such, potential interactions and their possible cellular ramifications are discussed.

Amino acid substitutions of coiled-coil protein Tpr abrogate anchorage to the nuclear pore complex but not parallel, in-register homodimerization

Tpr is a protein component of nuclear pore complex (NPC)-attached intranuclear filaments. Secondary structure predictions suggest a bipartite structure, with a large N-terminal domain dominated by heptad repeats (HRs) typical for coiled-coil--forming proteins. Proposed functions for Tpr have included roles as a homo- or heteropolymeric architectural element of the nuclear interior. To gain insight into Tpr's ultrastructural properties, we have studied recombinant Tpr segments by circular dichroism spectroscopy, chemical cross-linking, and rotary shadowing electron microscopy. We show that polypeptides of the N-terminal domain homodimerize in vitro and represent alpha-helical molecules of extended rod-like shape. With the use of a yeast two-hybrid approach, arrangement of the coiled-coil is found to be in parallel and in register. To clarify whether Tpr can self-assemble further into homopolymeric filaments, the full-length protein and deletion mutants were overexpressed in human cells and then analyzed by confocal immunofluorescence microscopy, cell fractionation, and immuno-electron microscopy. Surplus Tpr, which does not bind to the NPC, remains in a soluble state of approximately 7.5 S and occasionally forms aggregates of entangled molecules but neither self-assembles into extended linear filaments nor stably binds to other intranuclear structures. Binding to the NPC is shown to depend on the integrity of individual HRs; amino acid substitutions within these HRs abrogate NPC binding and render the protein soluble but do not abolish Tpr's general ability to homodimerize. Possible contributions of Tpr to the structural organization of the nuclear periphery in somatic cells are discussed.

The Raf signal transduction cascade as a target for chemotherapeutic intervention in growth factor-responsive tumors

This review focuses on the Ras-Raf-mitogen-activated protein kinase kinase (MEK)-extracellular signal-regulated kinase (ERK) signal transduction pathway and the consequences of its unregulation in the development of cancer. The roles of some of the cell membrane receptors involved in the activation of this pathway, the G-protein Ras, the Raf, MEK and ERK kinases, the phosphatases that regulate these kinases, as well as the downstream transcription factors that become activated, are discussed. The roles of the Ras-Raf-MEK-ERK pathway in the regulation of apoptosis and cell cycle progression are also analyzed. In addition, potential targets for pharmacological intervention in growth factor-responsive cells are evaluated.

Mitogen-activated protein kinase: conservation of a three-kinase module from yeast to human

Mitogen-activated protein kinases (MAPK) are serine-threonine protein kinases that are activated by diverse stimuli ranging from cytokines, growth factors, neurotransmitters, hormones, cellular stress, and cell adherence. Mitogen-activated protein kinases are expressed in all eukaryotic cells. The basic assembly of MAPK pathways is a three-component module conserved from yeast to humans. The MAPK module includes three kinases that establish a sequential activation pathway comprising a MAPK kinase kinase (MKKK), MAPK kinase (MKK), and MAPK. Currently, there have been 14 MKKK, 7 MKK, and 12 MAPK identified in mammalian cells. The mammalian MAPK can be subdivided into five families: MAPKerk1/2, MAPKp38, MAPKjnk, MAPKerk3/4, and MAPKerk5. Each MAPK family has distinct biological functions. In Saccharomyces cerevisiae, there are five MAPK pathways involved in mating, cell wall remodelling, nutrient deprivation, and responses to stress stimuli such as osmolarity changes. Component members of the yeast pathways have conserved counterparts in mammalian cells. The number of different MKKK in MAPK modules allows for the diversity of inputs capable of activating MAPK pathways. In this review, we define all known MAPK module kinases from yeast to humans, what is known about their regulation, defined MAPK substrates, and the function of MAPK in cell physiology.

Molecular segments of protein Tpr that confer nuclear targeting and association with the nuclear pore complex

Tpr is a 267-kDa protein of unknown function recently identified as a constitutive component of the nuclear pore complex (NPC2)-attached intranuclear filaments. Secondary structure predictions suggest that the protein is divided into a large, coiled-coil forming aminoterminal domain and a shorter, highly acidic carboxyterminal domain. To identify which of Tpr's molecular segments determine its specific intranuclear localization, we have constructed expression vectors encoding various Tpr deletion mutants as well as chimeric combinations of Tpr sequences with the soluble cytoplasmic protein pyruvate kinase. Following transfection of cultured mammalian cells, we have identified a short region within Tpr's carboxyterminal domain that is essential and sufficient to mediate nuclear import of Tpr and which can also confer nuclear accumulation of pyruvate kinase. Tpr deletion mutants that contain this nuclear targeting segment, but lack the aminoterminal domain, appear evenly dispersed throughout the nucleus without any noticeable association to the NPC. In contrast, the aminoterminal domain lacking the carboxyterminal region remains located within the cytoplasm, forming aggregate-like structures not associated with the nuclear envelope. However, when tagged to Tpr's short nuclear targeting segment or to the nuclear localization signal of the SV40 large T protein, the aminoterminal domain is imported into the nucleus, where it then associates with the NPC. This association is mediated by shorter molecular segments within the aminoterminal domain which contain clusters of heptad repeats, whereas other regions are dispensable. This assignment of different topogenetic properties to distinct molecular segments of Tpr will now allow the design of future experiments to study the protein's structural properties further and determine its actual function.

A protein kinase Cdelta-binding protein SRBC whose expression is induced by serum starvation

West-Western screening of a cDNA expression library using 32P-labeled, autophosphorylated protein kinase Cdelta (PKCdelta) as a probe, led us to identify cDNA clones encoding a PKCdelta-binding protein that contains a leucine zipper-like motif in its N-terminal region and two PEST sequences in its C-terminal region. This protein shows overall sequence similarity (43.3%) to the serum deprivation response (sdr) gene product, and we named it SRBC (sdr-related gene product that binds to c-kinase). PKCdelta binds to the C-terminal half of SRBC through the regulatory domain and phosphorylates it in vitro. In COS1 cells, the phosphorylation of over-expressed SRBC is stimulated by 12-O-tetradecanoylphorbol-13-acetate and further enhanced by the over-expression of PKCdelta. The mRNA for SRBC is detected in a wide variety of cultured cell lines and tissues and is strongly induced by serum starvation. Furthermore, SRBC mRNA is induced during retinoic acid-induced differentiation of P19 cells. These results suggest that SRBC serves as a substrate and/or receptor for PKC and might be involved in the control of cell growth mediated by PKC.

Rab3 reversibly recruits rabphilin to synaptic vesicles by a mechanism analogous to raf recruitment by ras

GTP activates the interaction between the synaptic vesicle proteins rabphilin and rab3. This raises the question of whether rabphilin is a resident vesicle protein that recruits rab3 in a stage-dependent fashion, or if it is instead an effector protein recruited by rab3. We now show that rabphilin, like rab3, dissociates from synaptic vesicles after exocytosis in a manner requiring both Ca2+ and membrane fusion. Rabphilin interacts with GTP-rab3 via a N-terminal domain comprising a novel Zn2+(-)finger motif, and this interaction is essential for rabphilin binding to synaptic vesicles. Thus, in the same way that ras recruits raf to the plasma membrane, rab3 reversibly recruits rabphilin to synaptic vesicles in a stage-dependent manner. These results reveal an unexpected similarity between the molecular mechanisms by which small G protein function in recruiting effector proteins to membranes during membrane traffic and signal transduction.

Nuclear pore complex proteins

The nuclear envelope forms the boundary between the nucleus and the cytoplasm and as such regulates the exchange of macromolecules between the two compartments. The channels through the nuclear envelop that actually mediate this macromolecular traffic are the nuclear pore complexes. These are extremely elaborate structures which in vertebrate cells exhibit a mass of approximately 120 MDa. They are thought to be composed of as many as 100 distinct polypeptide subunits. A major challenge in the field of nucleocytoplasmic transport is to identify these subunits and to determine their functions and interactions in the context of the three-dimensional structure of the nuclear pore complex. It is the aim of this review to summarize what is currently known of the 20 or so nuclear pore complex proteins that have been described in either vertebrate or yeast cells.

Patterns of gene expression along the crypt-villus axis in mouse jejunal epithelium

BACKGROUND

There is considerable interest in gene expression along the crypt-villus axis of the small intestinal epithelium, particularly in the identification of genes expressed in intestinal crypts.

METHODS

In an attempt to identify crypt-expressed genes, single-stranded cDNA made from normal mouse jejunal epithelium was used in subtractive hybridization against single-stranded cDNA from epithelium from which crypt cells were depleted by 2,000 rads of gamma irradiation. Partial DNA sequence and in situ hybridization of 72 resulting clones were determined.

RESULTS

The sequence of 45 clones matched previously published genes. Gene expression patterns fell into three categories: expression throughout the crypt-villus axis, expression restricted to the villus, and expression restricted to the crypt. Clones in the first two categories could be further divided into three subgroups: those with uniform expression, those with an increasing gradient of expression, and those with a decreasing gradient of expression along the crypt-villus axis. Twenty two clones showed a stronger expression in crypt and lower villus cells, four of these were differentially localized to the crypt. Two of the crypt localized clones were uniformly expressed throughout the crypt, expression of one was stronger in the lower crypt, and expression of the remaining clone was enhanced Paneth cells. We report the full-length cDNA sequence of the Paneth-cell-enhanced clone.

CONCLUSIONS

The screen isolated crypt-expressed genes that may prove useful tools in the study of crypt biology. In a companion report, we characterize one of the crypt clones.

Spatial and temporal changes in signal transduction pathways during LTP

Following LTP induction in freely moving rats, in situ hybridization revealed discrete changes in the expression of one isoform in each of four families of serine/threonine kinases constitutively expressed in the dentate gyrus of the hippocampus. Expression of the alpha isoform of CaMKII showed a transient increase over the soma and a more persistent increase over the dendritic field of dentate granule cells. Of the PKC isoforms, only gamma PKC was up-regulated substantially 2 hr after LTP induction, declining to control levels 48 hr later. An increase in the expression of mRNA for ERK2 and raf-B was seen at 24 hr only. These results show that, during the maintenance phase of LTP in the hippocampus, there are selective increases in the expression of serine/threonine kinases and that these increases have specific and characteristic temporal and spatial profiles.

A new yeast gene with a myosin-like heptad repeat structure

We isolated a gene encoding a 218 kDa myosin-like protein from Saccharomyces cerevisiae using a monoclonal antibody directed against human platelet myosin as a probe. The protein sequence encoded by the MLP1 gene (for myosin-like protein) contains extensive stretches of a heptad-repeat pattern suggesting that the protein can form coiled coils typical of myosins. Immunolocalization experiments using affinity-purified antibodies raised against a TrpE-MLP1 fusion protein showed a dot-like structure adjacent to the nucleus in yeast cells bearing the MLP1 gene on a multicopy plasmid. In mouse epithelial cells the yeast anti-MLP1 antibodies stained the nucleus. Mutants bearing disruptions of the MLP1 gene were viable, but more sensitive to ultraviolet light than wild-type strains, suggesting an involvement of MLP1 in DNA repair. The MLP1 gene was mapped to chromosome 11, 25 cM from met1.

B-raf oncogene: activation by rearrangements and assignment to human chromosome 7

cDNA clones presumably containing a transforming gene were isolated from transformed NIH3T3 cells, which were obtained by the transfection of DNA from peripheral blood lymphocytes of a familial adenomatous polyposis patient. Sequence analysis of the cDNA clones showed that the gene contained an activated B-raf, the 5' half of which was replaced by the human small nuclear ribonucleoprotein E protein gene and an unknown gene. A partial genomic physical map of the transforming gene was made on the basis of the physical map of the cDNA clones, indicating that rearrangements had occurred during the transfection. The human B-raf gene was shown to be located on chromosome 7 by Southern blotting analysis of rodent-human somatic cell hybrid DNA using the B-raf cDNA as a probe.

On the molecular mechanism of the circadian clock: The 64000-Mr protein of Chlamydomonas reinhardtii might be related to the biological clock

Labelling of Chlamydomonas reinhardtii cells with [(35)S] methionine led to the detection of a 64-kDa polypeptide which is synthesized according to a circadian rhythm. The change in synthesis rate could be demonstrated to exist under constant dim-light conditions as well as in darkness. Maximum synthesis of the 64-kDa polypeptide occurred at about 10 h after onset of constant conditions, and the period length of its oscillation was about 29 h. The 64-kDa polypeptide was synthesized on 80S ribosomes as shown by experiments in which cycloheximide and chloramphenicol were supplied to the cultures. Peptide-microsequence analysis yielded an N-terminal sequence of 14 amino acids. No significant homology to any other known polypeptide could be demonstrated in searches of current databases. The possible role of the 64-kDa polypeptide and its relationship to the biological clock is discussed.

PTC is a novel rearranged form of the ret proto-oncogene and is frequently detected in vivo in human thyroid papillary carcinomas

We recently detected a novel activated oncogene by transfection analysis on NIH 3T3 cells in five out of 20 primary human thyroid papillary carcinomas and in the available lymph node metastases. We designated this transforming gene PTC (for papillary thyroid carcinoma). Here we describe the molecular cloning and sequencing of the gene. The new oncogene resulted from the rearrangement of an unknown amino-terminal sequence to the tyrosine kinase domain of the ret proto-oncogene. This gene rearrangement was detected in all of the transfectants and in all of the original tumor DNAs, but not in normal DNA of the same patients, thus indicating that this genetic lesion occurred in vivo and is specific to somatic tumors. Moreover, the transcript coded for by the fused gene was detected in an additional PTC-positive human papillary carcinoma for which mRNA was available.

Expression of c-myc, c-raf-1, and c-Ki-ras in azaserine-induced pancreatic carcinomas and growing pancreas in rats

We examined the pattern of expression of several proto-oncogenes during nonneoplastic growth and in acinar cell neoplasms in the rat pancreas. The levels of c-myc, c-raf-1, and c-Ki-ras mRNAs were increased in regenerating pancreata following surgical partial pancreatectomy and following administration of camostat. We also investigated proto-oncogene expression associated with the progression of pancreatic cancers in azaserine-treated rats. Injection of a single dose (30 mg/kg) of azaserine (O-diazoacetyl-L-serine) to 14-d-old rats leads to a variety of neoplastic lesions in the rat pancreas. Total RNA was isolated from lesions in various stages of tumor progression, including adenomas, carcinomas in situ, and invasive carcinomas. We observed increased expression of c-myc, c-raf-1, and c-Ki-ras in azaserine-induced adenomas and carcinomas. Actin expression was also increased in these tissues, whereas amylase expression was variable. However, when compared to the normal growing pancreas, the level of proto-oncogene expression in the adenomas and carcinomas was disproportionate to the degree of cellular division in those tissues. Thus, the alterations induced by azaserine apparently caused a deregulated increase in expression of cellular oncogenes associated with growth regulation.

Expression of c-raf-1 and A-raf-1 during differentiation of 3T3-L1 preadipocyte fibroblasts into adipocytes

The objective of this study was to examine the expression of the c-raf-1 and A-rat-1 protooncogenes during differentiation of 3T3-L1 preadipocytes into adipocytes. At confluence, prior to initiation of differentiation c-raf and A-raf steady state mRNA levels were low. Expression of c-raf and A-raf began to increase 72 hours following initiation of differentiation by treatment with differentiation medium, reaching a maximum increase of 3 to 6-fold and 3 to 4-fold respectively by 190 hours. The increase of c-raf and A-raf steady state message levels occurred concomitant with the onset of differentiation as indicated by increased levels of glycerol-3-phosphate dehydrogenase mRNA. These changes were compared with those for several other protooncogene mRNAs including c-myc, c-fos, H-ras and histone H3. These results are the first to show increase expression of the raf protooncogenes during terminal differentiation rather than in association with proliferation.

raf involvement in the simultaneous genetic transfer of the radioresistant and transforming phenotypes

We examined a human Alu+ mouse tertiary transformant derived from a noncancerous skin fibroblast cell line which exhibits the unique characteristic of being resistant to the killing effects of ionizing radiation. This transformed cell line was found to contain activated human c-raf-1, and demonstrated an increased level of radioresistance indicating the simultaneous transfer of both the transforming and radiation-resistant phenotypes. We have also found a relationship between the presence of activated oncogenes, specifically those with serine/threonine kinase activity and the radioresistant phenotype.

Expression of c-raf-1 and A-raf-1 during regeneration of rat liver following surgical partial hepatectomy

The major objective of this study was to investigate the expression of members of the raf family of proto-oncogenes during rat liver regeneration. The steady-state level of expression of both c-raf-1 and A-raf-1 increased three- to fivefold 18-24 h following partial hepatectomy, and it returned to basal levels by 72 h. Expression of c-myc and Ha-ras mRNA was increased at 3 and 18-24 h, respectively, confirming previous reports. Increased steady-state levels of c-raf-1, A-raf-1, and Ha-ras mRNA were also detected in hepatocytes isolated from rat liver 24 h after partial hepatectomy. Thus, elevated expression of the raf genes closely correlated with that of Ha-ras, beginning at 12 h and reaching maximal levels during the first peak of DNA synthesis following partial hepatectomy.

Rat c-raf oncogene is located on chromosome 4 and may be activated by sequences from chromosome 13

Activated forms of the protooncogene c-raf have been found to transform established lines of rodent fibroblasts after transfection with DNA from several human and rat tumors. Using Southern blot analysis of DNAs from rat x mouse somatic cell hybrids, we have mapped c-raf to rat chromosome 4. An exogenous sequence that was found juxtaposed to c-raf within transforming DNA originally derived from a rat hepatocellular carcinoma was localized to chromosome 13.

Expression of human c-raf-1 oncogene proteins in E. coli

Full length and truncated versions of the human c-raf-1 cDNA were cloned into the inducible E. coli expression vector pJL6. C-raf proteins of 73 kD, 57 kD and 39 kD were produced upon induction. p73 differs from normal p73 c-raf by deletion of the two first N-terminal amino acids and their replacement by 16 amino acids encoded by the vector. The p57 and p39 represent N-terminal deletions which leave the transforming protein kinase domain intact. These proteins could be readily purified from E. coli lysates by immunoprecipitation with raf-specific antisera.