Chemoproteomics-based kinome profiling and target deconvolution of clinical multi-kinase inhibitors in primary chronic lymphocytic leukemia cells.

The pharmacological induction of apoptosis in neoplastic B cells presents a promising therapeutic avenue for the treatment of chronic lymphocytic leukemia (CLL). We profiled a panel of clinical multi-kinase inhibitors for their ability to induce apoptosis in primary CLL cells. Whereas inhibitors targeting a large number of receptor and intracellular tyrosine kinases including c-KIT, FLT3, BTK and SYK were comparatively inactive, the CDK inhibitors BMS-387032 and flavopiridol showed marked efficacy similar to staurosporine. Using the kinobeads proteomics method, kinase expression profiles and binding profiles of the inhibitors to target protein complexes were quantitatively monitored in CLL cells. The targets most potently affected were CDK9, cyclin T1, AFF3/4 and MLLT1, which may represent four subunits of a deregulated positive transcriptional elongation factor (p-TEFb) complex. Albeit with lower potency, both drugs also bound the basal transcription factor BTF2/TFIIH containing CDK7. Staurosporine and geldanamycin do not affect these targets and thus seem to exhibit a different mechanism of action. The data support a critical role of p-TEFb inhibitors in CLL that supports their future clinical development.

Proteomics-based strategies in kinase drug discovery.

Studies of drug action classically assess biochemical activity in settings which typically contain the isolated target only. Recent technical advances in mass spectrometry-based analysis of proteins have enabled the quantitative analysis of sub-proteomes and entire proteomes, thus initiating a departure from the traditional single gene--single protein--single target paradigm. Here, we review chemical proteomics-based experimental strategies in kinase drug discovery to analyse quantitatively the interaction of small molecule compounds or drugs with a defined sub-proteome containing hundreds of protein kinases and related proteins. One novel approach is based on 'Kinobeads'--an affinity resin comprised of a cocktail of immobilized broad spectrum kinase inhibitors--to monitor quantitatively the differential binding of kinases and related nucleotide-binding proteins in the presence and absence of varying concentrations of a lead compound or drug of interest. Differential binding is detected by high throughput and sensitive mass spectroscopy techniques utilizing isobaric tagging reagents (iTRAQ), yielding quantitative and detailed target binding profiles. The method can be applied to the screening of compound libraries and to selectivity profiling of lead compounds directly against their endogenously expressed targets in a range of cell types and tissue lysates. In addition, the method can be used to map drug-induced changes in the phosphorylation state of the captured sub-proteome, enabling the analysis of signalling pathways downstream of target kinases.

The new serine-threonine kinase, Qik, is a target of the Qin oncogene.

The winged helix transcription factor Qin is the avian homolog of the mammalian brain factor 1 (BF-1) and has the potential to act as an oncogenic protein. We used representational difference analysis to identify genes that are differentially expressed in chicken embryo fibroblasts (CEF) transformed by Qin. One of the up-regulated Qin targets identified in this analysis is a serine-threonine kinase termed Qik (Qin-induced kinase). Qik belongs to the AMPK/SNF1 kinase family. It is a ubiquitously expressed protein and is upregulated rapidly after a hormone-regulated form of Qin is activated. In vitro kinase tests demonstrate that Qik is capable of autophosphorylation. Elevated levels of Qik transcripts are also observed in Src-transformed cells, suggesting that Src and Qin share some targets.

v-Jun overrides the mitogen dependence of S-phase entry by deregulating retinoblastoma protein phosphorylation and E2F-pocket protein interactions as a consequence of enhanced cyclin E-cdk2 catalytic activity.

v-Jun accelerates G(1) progression and shares the capacity of the Myc, E2F, and E1A oncoproteins to sustain S-phase entry in the absence of mitogens; however, how it does so is unknown. To gain insight into the mechanism, we investigated how v-Jun affects mitogen-dependent processes which control the G(1)/S transition. We show that v-Jun enables cells to express cyclin A and cyclin A-cdk2 kinase activity in the absence of growth factors and that deregulation of cdk2 is required for S-phase entry. Cyclin A expression is repressed in quiescent cells by E2F acting in conjunction with its pocket protein partners Rb, p107, and p130; however, v-Jun overrides this control, causing phosphorylated Rb and proliferation-specific E2F-p107 complexes to persist after mitogen withdrawal. Dephosphorylation of Rb and destruction of cyclin A nevertheless occur normally at mitosis, indicating that v-Jun enables cells to rephosphorylate Rb and reaccumulate cyclin A without exogenous mitogenic stimulation each time the mitotic "clock" is reset. D-cyclin-cdk activity is required for Rb phosphorylation in v-Jun-transformed cells, since ectopic expression of the cdk4- and cdk6-specific inhibitor p16(INK4A) inhibits both DNA synthesis and cell proliferation. Despite this, v-Jun does not stimulate D-cyclin-cdk activity but does induce a marked deregulation of cyclin E-cdk2. In particular, hormonal activation of a conditional v-Jun-estrogen receptor fusion protein in quiescent, growth factor-deprived cells stimulates cyclin E-cdk2 activity and triggers Rb phosphorylation and DNA synthesis. Thus, v-Jun overrides the mitogen dependence of S-phase entry by deregulating Rb phosphorylation, E2F-pocket protein interactions, and ultimately cyclin A-cdk2 activity. This is the first report, however, that cyclin E-cdk2, rather than D-cyclin-cdk, is likely to be the critical Rb kinase target of v-Jun.

Nuclear endpoint of Wnt signaling: neoplastic transformation induced by transactivating lymphoid-enhancing factor 1.

The interaction between beta-catenin and LEF-1/TCF transcription factors plays a pivotal role in the Wnt-1 signaling pathway. The level of beta-catenin is regulated by partner proteins, including glycogen synthase kinase-3beta (GSK-3beta) and the adenomatous polyposis coli (APC) tumor suppressor protein. Genetic defects in APC are responsible for a heritable predisposition to colon cancer. APC protein and GSK-3beta bind beta-catenin, retain it in the cytoplasm, and facilitate the proteolytic degradation of beta-catenin. Abrogation of this negative regulation allows beta-catenin to translocate to the nucleus and to form a transcriptional activator complex with the DNA-binding protein lymphoid-enhancing factor 1 (LEF-1). This complex is thought to be involved in tumorigenesis. Here we show that covalent linkage of LEF-1 to beta-catenin and to transcriptional activation domains derived from the estrogen receptor or the herpes simplex virus protein VP16 generates transcriptional regulators that induce oncogenic transformation of chicken embryo fibroblasts. The chimeras between LEF-1 and beta-catenin or VP16 are constitutively active, whereas fusions of LEF-1 to the estrogen receptor are regulatable by estrogen. These experiments document the oncogenicity of transactivating LEF-1 and show that the transactivation domain normally provided by beta-catenin can be replaced by heterologous activation domains. These results suggest that the transactivating function of the LEF-1/beta-catenin complex is critical for tumorigenesis and that this complex transforms cells by activating specific LEF-1 target genes.

Glutaredoxin is a direct target of oncogenic jun.

We have analysed differential gene expression in v-jun-transformed chicken embryo fibroblasts (CEF) compared to normal CEF by using the directional tag PCR subtraction method. From a first generation of putative Jun targets four clones were selected for study; they are upregulated in jun-transformed cells. Three of these clones showed homology to known genes: glutaredoxin, growth associated protein (GAP)-43/neuromodulin, and phenobarbital-induced cytochrome P450. The expression of these genes was analysed in fibroblasts transformed by various oncogenes. Expression of the glutaredoxin mRNA could be induced by a Jun-estrogen receptor chimaera in the absence of de novo protein biosynthesis. Based on this observation we conclude that glutaredoxin is a direct target of v-Jun.

Hormone-regulatable neoplastic transformation induced by a Jun-estrogen receptor chimera.

The v-jun oncogene encodes a nuclear DNA binding protein that functions as a transcription factor and is part of the activator protein 1 complex. Oncogenic transformation by v-jun is thought to be mediated by the aberrant expression of specific target genes. To identify such Jun-regulated genes and to explore the mechanisms by which Jun affects their expression, we have fused the full-length v-Jun and an amino-terminally truncated form of v-Jun to the hormone-binding domain of the human estrogen receptor. The two chimeric proteins function as ligand-inducible transactivators. Expression of the fusion proteins in chicken embryo fibroblasts causes estrogen-dependent transformation.

DNA binding and transcriptional activation by the Ski oncoprotein mediated by interaction with NFI.

The Ski oncoprotein has been found to bind non-specifically to DNA in association with unindentified nuclear factors. In addition, Ski has been shown to activate transcription of muscle-specific and viral promoters/enhancers. The present study was undertaken to identify Ski's DNA binding and transcriptional activation partners by identifying specific DNA binding sites. We used nuclear extracts from a v-Ski-transduced mouse L-cell line and selected Ski-bound sequences from a pool of degenerate oligonucleotides with anti-Ski monoclonal antibodies. Two sequences were identified by this technique. The first (TGGC/ANNNNNT/GCCAA) is the previously identified binding site of the nuclear factor I (NFI) family of transcription factors. The second (TCCCNNGGGA) is the binding site of Olf-1/EBF. By electophoretic mobility shift assays we find that Ski is a component of one or more NFI complexes but we fail to detect Ski in Olf-1/EBF complexes. We show that Ski binds NFI proteins and activates transcription of NFI reporters, but only in the presence of NFI. We also find that homodimerization of Ski is essential for co-activation with NFI. However, the C-terminal dimerization domain of c-Ski, which is missing in v-Ski, can be substituted by the leucine zipper domain of GCN4.

Chromosomal localization of the four genes (NFIA, B, C, and X) for the human transcription factor nuclear factor I by FISH.

Nuclear Factor I (NFI) proteins constitute a family of dimeric DNA-binding proteins with very similar, possibly identical, DNA-binding specificity. They function as cellular transcription factors and as replication factors for adenovirus DNA replication. Diversity in this protein family is generated by multiple genes, differential splicing, and heterodimerization. To determine the chromosomal position of NFI genes in the human genome, we isolated partial cDNA sequences derived from four independent genes: NFIA, NFIB, NFIC, and NFIX. Corresponding clones of genomic DNA served as probes for fluorescence in situ hybridization on human metaphase chromosomes. The NFIA and NFIB genes map to positions 1p31.2-p31.3 and 9p24.1, respectively. The NFIC and the NFIX genes were both localized to position 19p13.3 in the order centromere-NFIX-NFIC-telomere. Comparison of the position of NFI genes and JUN genes revealed a close physical linkage between members of the NFI and JUN gene families in the human genome.

Nuclear factor I interferes with transformation induced by nuclear oncogenes.

The four nuclear factor I genes (NFI-A, NFI-B, NFI-C, and NFI-X) give rise to multiple isoforms by alternative splicing in many tissues. These NFI proteins cooperate with AP-1, Myc, and other transcription factors in regulating transcription of numerous cellular and viral genes. We have investigated the growth-regulatory potential of NFI by overexpressing cDNAs from chicken NFI genes -A, -B, -C, and -X in chicken embryo fibroblasts (CEF). None of the NFI cDNAs induced oncogenic transformation of CEF. However, overexpression of each of the NFI proteins caused similar morphological alteration of the cells, inducing them to become flattened and polygonal and to show increased adherence. The growth properties of these cells were similar to normal CEF. When these morphologically altered CEF were challenged by superinfection with oncogenic retroviruses, they were resistant to transformation by the nuclear oncogenes jun, fos, junD, myc, and qin but were readily transformed by cytoplasmic oncogenes src, mil/raf, ras, and fps. The NFI-A1 protein was able to alter transactivation by the cellular and viral Jun proteins in a promoter-dependent manner. The changes in cell morphology and reduced susceptibility to nuclear oncogenes were not seen with a carboxy-terminal truncation in the transactivation domain of NFI, suggesting that this region of the protein is essential for the observed effects. The dichotomy between the activities of nuclear and of cytoplasmic oncogenes in this system is discussed.

Transcription factor nuclear factor I proteins form stable homo- and heterodimers.

Nuclear factor I (NFI) proteins constitute a large family of eukaryotic DNA binding proteins. They are involved in viral and cellular aspects of transcriptional regulation and they are capable of stimulating adenovirus initiation of replication. Using in vitro translated NFI proteins encoded by four different chicken NFI genes, we have detected homodimers as well as heterodimers for all combinations tested. The formation of heterodimers was critically dependent on cotranslation, indicating stable dimer formation in the absence of DNA. The unrestricted heterodimerization of NFI proteins adds, beside gene diversity and alternative splicing, another level of diversity to this protein family.

The genes for transcription factor nuclear factor I give rise to corresponding splice variants between vertebrate species.

Nuclear Factor I (NFI) proteins are DNA binding proteins functioning as transcription and replication factors. As part of a study of the diversity of the Nuclear Factor I protein family, we isolated and sequenced seven NFI cDNA clones from a chicken promacrophage library. Five of these clones are derived from the NFI-A gene, the other two from the NFI-C gene. Comparison of the deduced chicken NFI amino acid sequences with mammalian NFI sequences reveals that there are corresponding vertebrate isoforms, indicating a strong conservation of NFI structure during evolution. This finding leads to the prediction that more mammalian isoforms will be discovered corresponding to the chicken NFI variants reported here.

Gene product dsbA of bacteriophage T4 binds to late promoters and enhances late transcription.

Gene product 33 of phage T4 is known to be essential in late transcription. Upstream from gene 33 and overlapping its 5' terminal sequence by 20 bp, we identified an open reading frame coding for a binding protein for double-stranded DNA (DsbA). Gene product DsbA is composed of 89 amino acid residues with a Mr of 10376 kDa. We purified this protein to homogeneity from over-expressing cells. Gel retardation assays reveal that it binds to DNA and footprint analyses disclose that it interacts preferentially with T4 late promoter regions. At the sites of binding the protein introduces nicks in double-stranded DNA. In vitro transcription assays performed with T4 late modified RNA polymerase on restriction fragments harbouring a T4 late promoter region prove that gene product DsbA enhances transcription from these promoter regions in the presence of gene product 33. Gene dsbA is distinct from gene das which maps close to this genomic region.

Chicken NFI/TGGCA proteins are encoded by at least three independent genes: NFI-A, NFI-B and NFI-C with homologues in mammalian genomes.

Chicken TGGCA proteins belong to the ubiquitous, eukaryotic family of NFI-like nuclear proteins, which share an identical DNA binding specificity. They are involved in viral and cellular aspects of transcriptional regulation and they are capable of stimulating Adenovirus initiation of replication. Using microsequencing data from peptides of isolated proteins and PCR supported cloning, we have derived four cDNAs for NFI/TGGCA proteins, which are encoded by three separate chicken genes. Sequence alignments of NFI proteins from chicken and various mammalian species provide evidence for a common genetic equipment among higher eukaryotes, in which several related genes, employing each differential RNA splicing generate an unexpectedly large family of diverse NFI proteins. The extensive similarity of the amino acid sequence throughout the complete coding regions between products of the same gene type in different species indicates a uniform selection pressure on all protein parts, also on those outside the DNA-binding domain.

The human lysozyme gene. Sequence organization and chromosomal localization.

We have isolated two overlapping recombinant lambda-phage clones from a genomic lambda-EMBL3 library containing 25 kb of the human lysozyme gene region. Furthermore a full-lenght human lysozyme cDNA clone of 1.5 kb was isolated from a human placenta cDNA library. Nucleotide sequences of the entire structural gene and the cDNA clone were determined. The human lysozyme gene spans 5856 bp and its sequence organization with four exons and three introns is homologous to the chicken lysozyme gene and the human alpha-lactalbumin gene. Human and chicken lysozyme genes differ mainly in the size of their introns and 3' non-coding region. Four Alu repetitive elements were found in the human lysozyme gene, one in each intron and one on the fourth exon. Lysozyme transcripts of 1.6 kb and 0.6 kb in size were detected in human myeloid cell lines U-937, HL-60 and THP-1 and surprisingly in human hepatoma cell lines HepG2 and Hep3B. The lysozyme gene locus was assigned to human chromosome 12 by hybridization to a panel of DNAs from human-rodent somatic cell hybrids.

Biochemical markers of bone turnover, intact serum parathyroid horn and renal calcium excretion in patients with pseudohypoparathyroidism and hypoparathyroidism before and during vitamin D treatment.

In addition to the well-documented hyporesponsiveness of the kidney, resistance to parathyroid hormone (PTH) has been postulated for bone in pseudohypoparathyroidism type I (PHP). In some of these patients reduced bone density and even frank osteitis fibrosa suggest osteoclastic overactivity. To address the possibility that the skeletal system of patients with PHP may be affected by their increased PTH secretion we measured intact serum PTH and three biochemical markers of bone turnover in a large number of patients with PHP (n = 20). The results were compared with subjects with low (hypoparathyroidism, HP n = 29), normal (controls, n = 31) and high (primary hyperparathyroidism, 1 degree HPT, n = 13) PTH secretion. Both markers of osteoblastic bone formation, alkaline phosphatase activity and osteocalcin concentration in serum, and one index of osteoclastic bone degradation, the urinary hydroxyproline/creatinine ratio (OH-P/Cr), were decreased in HP and increased in 1 degree HPT, whereas only OH-P/Cr was elevated in patients with PHP. Although intact serum PTH was significantly more increased in PHP than in 1 degree HPT, the markers of bone turnover were not significantly different in these two groups, suggesting some bone resistance in the patients with PHP. In these subjects intact serum PTH was elevated even at normocalcaemia during vitamin D treatment with a negative correlation with the respective serum calcium concentration (r = -0.69, P less than 0.001), indicating an elevated set-point for the suppression of their parathyroid glands. OH-P/Cr was negatively related to serum calcium in PHP, it normalized in most patients during normocalcaemia induced by vitamin D treatment.(ABSTRACT TRUNCATED AT 250 WORDS)

[Disorders of calcium and bone metabolism in glucocorticoid treatment]. / Kalzium- und Knochenstoffwechselstörungen unter Glukokortikoid-Behandlung.

The effects of glucocorticoids on calcium and bone metabolism were investigated in 11 children (aged 6 months to 13 years) who were treated with dexamethasone, prednisolone and depot-ACTH because of different disorders. Alkaline phosphatase activity and osteocalcin in serum, representing indices of osteoblastic bone synthesis, and urinary hydroxyproline in relation to creatinine in morning fasting urine specimens, an index of osteoclastic bone degradation, decreased by 53-61% from baseline (P less than 0.01), with a highly significant relationship of all 3 indices to each other. Additional influences of glucocorticoids were hyperphosphaturia due to decreased renal phosphate reabsorption not mediated by secondary hyperparathyroidism, as well as marked hypercalciuria. As the consequence of the present study the following prophylactic or therapeutic recommendations are given during steroid-treatment: 1. Approvement of the negative balance of calcium and phosphate by correcting the hypercalciuria with hydrochlorothiazide, and the hypophosphatemia with oral phosphate and 2. in elder children with osteoporosis, stimulation of the decreased osteoblastic bone formation by sodium fluoride.