Computational detection of allergenic proteins attains a new level of accuracy with in silico variable-length peptide extraction and machine learning.

The placing of novel or new-in-the-context proteins on the market, appearing in genetically modified foods, certain bio-pharmaceuticals and some household products leads to human exposure to proteins that may elicit allergic responses. Accurate methods to detect allergens are therefore necessary to ensure consumer/patient safety. We demonstrate that it is possible to reach a new level of accuracy in computational detection of allergenic proteins by presenting a novel detector, Detection based on Filtered Length-adjusted Allergen Peptides (DFLAP). The DFLAP algorithm extracts variable length allergen sequence fragments and employs modern machine learning techniques in the form of a support vector machine. In particular, this new detector shows hitherto unmatched specificity when challenged to the Swiss-Prot repository without appreciable loss of sensitivity. DFLAP is also the first reported detector that successfully discriminates between allergens and non-allergens occurring in protein families known to hold both categories. Allergenicity assessment for specific protein sequences of interest using DFLAP is possible via ulfh@slv.se.

Retinoids as ligands and coactivators of protein kinase C alpha.

Whereas retinoic acids control nuclear events, a second class of retinol metabolites, that is, the hydroxylated forms exemplified by 14-hydroxy-retro-retinol (HRR), operate primarily in the cytoplasm. They function as regulatory cofactors for cell survival/cell death decisions. In accordance with these biological aspects, we demonstrate that these retinoids bound protein kinase C (PKC) alpha with nanomolar affinity and markedly enhance the activation of PKC alpha and the entire downstream MAP kinase pathway by reactive oxygen species. HRR was 10 times more efficient than retinol, and the optimum doses are 10-7 and 10-6 M, respectively. PKC alpha activation was reversed rapidly by imposition of reducing conditions. The retinoid binding site was mapped to the first cysteine-rich region in the regulatory domain, C1A, yet was distinct from the binding sites of diacylglycerol and phorbol esters. The C1B domain bound retinoids poorly. The emerging theme is that retinoids serve as redox regulators of protein kinase C.

The cysteine-rich regions of the regulatory domains of Raf and protein kinase C as retinoid receptors.

Vitamin A and its biologically active derivatives, the retinoids, are recognized as key regulators of vertebrate development, cell growth, and differentiation. Although nuclear receptors have held the attention since their discovery a decade ago, we report here on serine/threonine kinases as a new class of retinoid receptors. The conserved cysteine-rich domain of the NH(2)-terminal regulatory domains of cRaf-1, as well as several select domains of the mammalian protein kinase C (PKC) isoforms alpha, delta, zeta, and mu, the Drosophila and yeast PKCs, were found to bind retinol with nanomolar affinity. The biological significance was revealed in the alternate redox activation pathway of these kinases. Retinol served as a cofactor to augment the activation of both cRaf and PKC alpha by reactive oxygen, whereas the classical receptor-mediated pathway was unaffected by the presence or absence of retinol. We propose that bound retinol, owing to its electron transfer capacity, functions as a tag to enable the efficient and directed redox activation of the cRaf and PKC families of kinases.

F-actin as a functional target for retro-retinoids: a potential role in anhydroretinol-triggered cell death.

The retro-retinoids, metabolites of vitamin A (retinol), belong to a family of lipophilic signalling molecules implicated in regulation of cell growth and survival. Growth-promoting properties have been ascribed to 14-hydroxy-retro-retinol (14HRR), while anhydroretinol (AR) was discovered to act as a natural antagonist triggering growth arrest and death by apoptosis. Based on morphological studies and inhibition of apoptosis by the kinase blocker, herbimycin A, it has been suggested that retro-retinoids exhibit their function in the cytosolic compartment. F-actin emerged as a functional target for retro-retinoid action. By FACS analysis and fluorescence microscopy of phalloidin-FITC labeled cells we demonstrated that F-actin reorganization was an early event in AR-triggered apoptosis. Fluorescence images of AR-treated fibroblasts displayed short, thick, stick-like and punctate structures, and membrane ruffles at the cell periphery along with an increased diffuse staining pattern. Reversal of the AR effect by 14HRR or retinol indicates that F-actin is a common site for regulation by retro-retinoids. Inhibition of both cell death and actin depolymerisation by bcl-2 implies that cytoskeleton reorganization is downstream of bcl-2-related processes. Furthermore, stabilization of microfilaments by jasplakinolide increased the survival potential of AR treated cells, while weakening the cytoskeleton by cytochalasin B abetted apoptosis. Thus the cytoskeleton is an important way station in a communication network that decides whether a cell should live or die.

The beta-gal interferon assay: a new, precise and sensitive method.

Cells of a human glioblastoma line were stably transfected with a glial fibrillary acidic protein (GFAP) promoter sequence/lacZ reporter gene. Following this modification, they produced Escherichia coli beta-galactosidase constitutively in amounts that could be measured through their conversion of an added fluorophore into a product readily estimated by fluorimetry. Human interferons (IFN) selectively and in a dose-dependent manner reduce the formation of beta-galactosidase in this system. We have used it as the basis for a novel assay that is sensitive (4-40 pg/ml), precise, completed in 30 h, and applicable to both type I and type II human IFNs. Statistical analysis showed interassay relative standard deviations ranging from 5% to 11%, and most individual assays revealed potencies with limits of error within 85%-115%. Neither partially trypsin-digested IFN nor the other cytokines and mitogens we tested reacted in this system, except for tumor necrosis factor-alpha (TNF-alpha). The high selectivity was further shown by the loss of response to IFN in the presence of the appropriate specific anti-IFN or anti-IFN-gamma receptor antibodies.

In vitro cellular responses to cytokines and erythropoietin.

Cytokines and polypeptide hormones act through high-affinity binding to cognate transmembrane receptor molecules, expressed on target cells. The impact of such ligand molecules is conveyed to the cell nucleus by specific signal transduction mechanisms and is ultimately manifested as changes in gene expression, largely accomplished by transcription-regulatory factors. Depending on target cell maturation and receptor signalling pathways, cell-cycle progression or growth inhibition may follow from ligand/receptor interactions. We have employed cellular growth as an endpoint for potency determination of several human bioactive substances, such as interferons (IFNs), IL-2, G-CSF, GM-CSF and erythropoietin (Epo), using murine or human cell lines as indicators. The conversion of the tetrazolium salt MTT by mitochondrial reductase to blue formazan served as an endpoint in such estimations. In addition to a cellular growth suppression IFN assay, a reporter gene-modified human glioblastoma line was devised to provide an implement for high-throughput potency assessment of interferons. The bioassay systems were all designed according to the parallel line assay model and were subjected to extensive validation procedures. Both intra- and inter-assay variations were consistently within the range of immunometric counterparts; hence precision and reproducibility do not need to be compromised when using biological determination methods. Furthermore, the advantage of monitoring downstream signal transduction effects of ligand binding, particularly over immunometry, is evident since it reflects a pharmacodynamic cellular response. The assays were operating in the pM range and their sensitivity could hence compete with immunometric counterparts. When applicable, the aforementioned approaches were combined with physicochemical characterization of the respective ligands, which further enhanced the physiological relevance of the cellular readout. Accordingly, such two-part assays should provide alternatives to traditional in vivo activity determinations of biological substances.

Retro-retinoids in regulated cell growth and death.

Vitamin A serves as a prohormone from which three classes of active metabolites are derived: the aldehydes, the carboxylic acids, and the retro-retinoids. Although these three classes are united under the rubric of signal transduction, they act by different molecular mechanisms: the 11-cis-retinaldehydes combine with opsin to form the universal visual pigments and the retinoic acids form ligands for transcription factors, whereas the retro-retinoids, as shown here, intersect with signal transduction at a cytoplasmic or membrane site. The retro-retinoid, anhydroretinol (AR), has long been known to act as a growth inhibitor in lymphocytes, whereas 14-hydroxy-4,14-retro-retinol (14-HRR) is required for normal lymphocyte proliferation. A mutually reversible relationship exists between these two retro-retinoids as one can reverse the effects of the other when given in pharmacological doses. The common explanation for reversible inhibition is competition for a shared receptor. We now provide evidence that when AR is given to T cells unmitigated by 14-HRR, rapid cell death can occur. The circumstances are closely related to nonclassical forms of apoptosis: within 2 h of AR administration the T cells undergo widespread morphological changes, notably surface blebbing and ballooning and, inevitably, bursting. In contrast, nuclear changes are comparatively mild, as indicated by absence of chromatin condensation and overt DNA cleavage to discrete nucleosomal fragments, although DNA nicks are readily discernible by terminal deoxynucleotidyl transferase assay. What further distinguishes the AR-induced form of apoptosis from classical ones is a lack of requirements of messenger RNA and protein synthesis, suggesting that the events leading to cell death are primarily initiated and play themselves out in the cytoplasm. This view is further reinforced by the finding that herbimycin A can prevent the onset of programmed cell death. The importance of our findings is that they strongly suggest a second messenger role for vitamin A metabolites in the cytoplasmic realm that has not been seen previously. These findings are entirely compatible with a general notion that in a cell requiring multiple coordinated signals for survival, the provision of an unbalanced signal can initiate programmed cell death. Collectively, our data also challenge the paradigm that retinoids (outside vision) solely mediate their function via the steroid/ retinoic acid receptor family of nuclear transcription factors. Instead, a mode of action in the cytoplasmic realm akin to one attributed to other small lipophilic second messenger molecules, such as diacyl glycerol or ceramide, may apply to retro-retinoids.

In vitro bioassay for human erythropoietin based on proliferative stimulation of an erythroid cell line and analysis of carbohydrate-dependent microheterogeneity.

The human erythroleukemia cell line TF-1 was employed for the determination of proliferative stimulation induced by recombinant human erythropoietin (rhEpo). Potencies of various intact and sugar-trimmed rhEpo preparations were estimated using the International Standard for Human r-DNA-derived Epo (87/684) as a reference for activity. The cellular response was measured in a multi-channel photometer using a colorimetric microassay, based on the metabolism of the tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide to formazan, by viable cells. The linear part of the log dose-response relationship encompassed 2.5-90 pM and activity of rhEpo preparations was measured at doses between 3 and 60 pM. The assay was designed as a parallel line test, using three or four concentrations for potency determinations, which fulfills pharmacopoeial requirements for assay validity. Inter-assay relative standard deviation varied between 4.1% and 12.6% and most assays revealed potencies with limits of error within 87-113%. In order to acquire an additional means for an efficient probing of physiologically relevant features of rhEpo, a luminiscence-dependent Western detection system, based on a combined isoelectric focusing/sodium dodecyl sulphate-polyacrylamide gel electrophoresis separation, was established. As opposed to conventional electrophoresis the two dimensional approach enabled the disclosure of minor truncations in the rhEpo-attached glycan moieties using picomolar quantities of the hormone. Moreover, the separated isoforms of rhEpo were quantified by computer-assisted densitometry and compared with the 87/684 standard. Accordingly, results obtained by the cellular response were balanced against the general pattern observed and the relative amounts of separated rhEpo isomers as determined by the quantitative Western analysis. The method described should be suitable for potency assessments of pharmaceutical formulations of rhEpo.

In vitro bioassay with enhanced sensitivity for human granulocyte colony-stimulating factor.

A method for the determination of human granulocyte colony-stimulating factor (hG-CSF) activity, based on stimulation of cellular proliferation, was developed using a subclone of the murine myeloid leukemia cell line NFS-60, with an improved sensitivity for hG-CSF, as indicator. The optimal range for quantitative analysis of hG-CSF was about 4-60 pg ml-1. The stimulatory effect was measured by a colorimetric microassay: the optical density of formazan, which is produced by viable cells from 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), was obtained by reading plates in a multi-channel photometer. The assay was designed as a five-dose parallel line test, employing three or four doses for potency determinations, which fulfil pharmacopoeial requirements for assay validity. Inter-assay relative standard deviation (RSD) varied between 5.2 and 12.0%. Most assay experiments revealed potencies within limits of error of 90-110% and the mean index of precision value was 0.057. The recently developed yeast cell-derived International Standard (88/502) served as a reference for activity of rhG-CSF. Specificity of the assay was demonstrated by absence of response upon exposure to a panel of biomolecules, including recombinant human interleukin-3, and by the suppression of growth stimulation in the presence of neutralizing anti hG-CSF antibodies. Potency readings of unglycosylated rhG-CSF were dependent on pH of assay medium with higher relative activities observed at pH 6.6 than at 7.4. Moreover, SDS-PAGE analysis of the carbohydrate-deficient preparation, following incubation at physiological pH, revealed several high molecular weight rhG-CSF bands and decreased monomeric form. The method described was found suitable for potency assessments of pharmaceutical formulations of hG-CSF.

Activation of the human NPY gene during neuroblastoma cell differentiation: induced transcriptional activities of AP-1 and AP-2.

During functional neuronal differentiation of human SH-SY5Y neuroblastoma cells, induced by 12-O-tetradecanoylphorbol-13-acetate (TPA), the mRNA expression of c-fos and c-jun displayed a synchronous and biphasic type of induction for both mRNAs, with an early transient (30 to 120 min) and a later (> 8 h) more persistent increase. This was coupled to increased in vitro DNA binding activity of cFos/cJun AP-1 heterodimers in SH-SY5Y nuclear extracts using the electrophoretic mobility shift assay. Functional AP-1 activity was demonstrated in differentiating SH-SY5Y cells by transient transfection assays using a TPA-responsive reporter plasmid. The second expression phase of these protooncogenes was paralleled by a sustained induction of neuronal differentiation markers, as exemplified by growth-associated protein 43 and neuropeptide tyrosine (NPY) mRNAs. DNA-protein interaction between an evolutionarily conserved region (-73 to -45) of the human NPY promoter, containing potential binding sites for AP-1, AP-2, and Sp1, and nuclear extracts prepared from untreated and TPA-treated SH-SY5Y cells revealed one complex (CI) that was unaffected and three complexes (CII to CIV) that were induced by TPA treatment. Competition for DNA binding using AP-1, AP-2, and Sp1 consensus sequences and an anti-cJun antibody, respectively, revealed cooperative interactions between AP-1, AP-2, and Sp1 transcription factors and the NPY promoter. In addition, TPA-mediated induction of AP-2 DNA binding activity to the NPY promoter was not dependent on increased AP-2 mRNA expression. This high degree of complexity presumably involved in NPY gene expression during neuronal differentiation of SH-SY5Y cells suggests productive cooperative interactions between multiple transcription factors.

Intracellular signaling activity of synthetic (14R)-, (14S)-, and (14RS)-14-hydroxy-4,14-retro-retinol.

14-Hydroxy-4,14-retro-retinol (14-HRR), first isolated from cultures of lymphoblastoid 5/2 and HeLa cells and characterized by NMR, UV, and CD, is a metabolite of retinol which promotes growth of B lymphocytes in culture and activation of T lymphocytes by antigen receptor-mediated signals. It is also produced by various tested cell lines: fibroblasts, leukemia, and Drosophila cells. 14-HRR is the first bioactive retro-retinoid to be discovered and, after retinal and retinoic acid, is the third intracellular messenger molecule derived from retinol. Physical properties and intracellular signaling activities of synthetic (14R)-HRR, (14S)-HRR, and racemic 14-HRR are described. CD spectra indicate that natural 14-HRR isolated previously was a mixture of enantiomers. B-cell survival and T-cell activation assays performed in the optimal range of (7-1.6) x 10(-7) M surprisingly showed that all 14-HRR compounds exhibit similar activity, with the 14R enantiomer exhibiting slightly higher activity in comparison to the 14S enantiomer. However, because of the semiquantitative nature of the assays, the conclusion as to which enantiomer is more active and which is the true ligand for the target receptor must await characterization of this protein.

Growth control or terminal differentiation: endogenous production and differential activities of vitamin A metabolites in HL-60 cells.

Vitamin A (retinol) is a prohormone that exerts its pleiotropic biological effects after conversion into multiple metabolites. In this report we describe the identification of three endogenous, retinolderived effector molecules, 14-hydroxy-retro-retinol (14-HRR), anhydroretinol (AR), and retinoic acid (RA) and a putative storage form of retinol, retinylesters (RE) in the human promyelocytic leukemia cell line HL-60. Exogenous application of the retinol metabolites in retinol-depleted serum-free cultures of HL-60 allowed the identification of unique cellular functions for each metabolite: 14-HRR is a growth factor for HL-60. AR is a functional antagonist of 14-HRR with growth-inhibiting activity, and RA is a potent inducer of granulocyte differentiation accompanied by growth arrest. Finally, intracellular RE serves as storage form allowing continuous production of 14-HRR when no external retinol is available.

Human GAP-43 Gene Expression: Multiple Start Sites for Initiation of Transcription in Differentiating Human Neuroblastoma Cells.

Phorbol ester treatment of human SH-SY5Y neuroblastoma cells, which leads to mature neuron-like cells with a sympathetic phenotype, induces outgrowth of neurites which are terminated by growth cones. The neurite extension is parallelled by an increased expression of the growth-associated protein, GAP-43. At the mRNA level, two GAP-43 mRNA species of 1.4 and 1.6 kb, respectively, were detected in SH-SY5Y cells. Both the low- and high-molecular-weight GAP-43 transcripts cosedimented with a polysomal fraction, indicating translation of both types of transcripts. To structurally characterize these GAP-43 mRNAs, several cDNA clones were isolated. The only difference identified corresponded to various size extensions in the 5'-untranslated region. A human genomic DNA fragment extending 1145 bp 5' of the GAP-43 translation start site, including a putative promoter region of the GAP-43 gene, was also characterized. Comparison of human and rat GAP-43 genomic sequences revealed an 85% identity between the first 900 bp 5' of translation start site. By RNase protection analysis, two clusters of putative transcription start sites, located approximately 200 bp apart, were identified. DNaseI footprinting analyses, using nuclear extracts prepared from untreated and TPA-treated SH-SY5Y cells, revealed specific footprints primarily detected in extracts prepared from differentiating cells. These clustered at positions immediately 5' of the two putative transcription start site regions. GAP-43 mRNA expression was finally studied using a probe which specifically recognizes the high-molecular-weight GAP-43 transcripts. Five tested human neuroblastoma cell lines and human fetal brain tissue expressed these transcripts. Furthermore, during differentiation of SH-SY5Y and LA-N-5 cells, both sizes of GAP-43 transcripts were transiently induced with the larger slightly preceeding the smaller mRNA species.

Protein kinase C remains functionally active during TPA induced neuronal differentiation of SH-SY5Y human neuroblastoma cells.

SH-SY5Y human neuroblastoma cells can be induced to differentiate into a neuronal phenotype by treatment with 12-O-tetradecanoylphorbol-13-acetate (TPA). In other cell systems, TPA treatment frequently leads to down-regulation of protein kinase C (PKC). However, we now report that TPA-treated and non-treated SH-SY5Y cells express PKC-alpha, but not PKC-beta and PKC-gamma, mRNA. Furthermore, only a slight down-regulation of the PKC-alpha protein could be seen during prolonged treatment with 16 nM TPA, the concentration giving optimal differentiation. In contrast, a higher concentration of TPA (1.6 microM) results in a poor neuronal differentiation and a complete down-regulation of PKC-alpha. PKC-alpha was rapidly translocated to the particulate fraction and remained membrane bound for at least 4 days during treatment with 16 nM TPA. In such cells a sustained increased level of the phosphorylated form of a 80,000 Dalton PKC-substrate was found. In addition to this sustained augmented phosphorylation, administration of fresh TPA at day 4 caused a small but reproducible further increased level of phosphorylated substrate. When the PKC activity was measured by the histone phosphorylation assay a substantial fraction of the initial enzyme activity could still be detected after 4 days of TPA treatment. Taken together, the data demonstrate that PKC remains functionally active during TPA induced differentiation of SH-SY5Y cells, which may suggest a continuous role for the enzyme during the differentiation process.

Retinoids are important cofactors in T cell activation.

Murine thymic T cells depleted of antigen-presenting cells proliferate poorly in response to crosslinking anti-CD3 monoclonal antibodies or concanavalin A when cultured in conventional fetal calf serum-containing serum. However, in a serum-free medium formulated to contain, in addition to basic ingredients, insulin, transferrin, albumin, linoleic acid (ITLB), and retinol, proliferation is vigorous. The presence of retinol is critical, because when omitted, cells do not become activated. The subsets of T cells proliferating with the assistance of retinol cofactor are both CD4+ and CD8+ thymic T cells, and CD4+ peripheral T cells. Mature CD8+ T cells of lymph nodes can also be activated in ITLB medium plus retinol, provided that interleukin 2 (IL-2) is added. Retinol needs to be present at the time when T cell receptor triggering is initiated, suggesting that early activation events (G0 to G1 transition) are dependent on retinol. It is currently less clear whether or not subsequent events associated with G1 to S phase transition also require the presence of retinol. 14-hydroxy-retroretinol (14HRR) is a metabolic product of retinol in lymphocytes, and this retinoid effectively supports T cell activation in conjunction with a mitogen in lieu of retinol. Thus, while retinol and its intracellular product, 14HRR, are unable to activate T cells on their own, they are important cofactors. The requirement for retinol in CD3-mediated T cell activation cannot be satisfied by retinoic acid or ILs-1, 2, 4, and 6, and tumor necrosis factor-alpha whereas interferon gamma can substitute for retinol. Our experiments are compatible with the idea that retinol, in the course of cellular activation, is converted to 14HRR, which is needed as intracellular messenger. If substantiated by molecular studies now underway, our data should lead to the description of a new signal pathway distinct from the retinoic acid signal pathway observed in nonlymphoid cells, but perhaps functioning by a similar mechanism, i.e., ligand-assisted transcriptional regulation.

src expression in small-cell lung carcinoma and other neuroendocrine malignancies.

The proto-oncogene c-src codes for two tyrosine kinases, pp60c-src and pp60c-srcN. The latter protein appears to be exclusively expressed in neurons and neuronally differentiated tumors. In cell lines derived from neuroblastoma and small-cell lung carcinoma, src expression correlates positively with neuroendocrine differentiation. However, pp60c-srcN is expressed only in highly differentiated neuroblastomas. Although c-src expression in neuroendocrine tumors probably reflects and is the result of the differentiation stage at which the tumors have been arrested, high c-src expression and kinase activities in non-neuroectodermal tumors, e.g., colon carcinoma, breast carcinoma, might instead be a part of the malignant phenotype and contribute to the development of these tumors.

A novel autoregulatory cytokine is required for the regulation of autoaggressive responses.

Limiting dilution studies indicate that cells with the potential to lyse autologous target cells exist in the peripheral blood of all normal individuals. In contrast to allocytotoxic cells, autocytolytic cells are down-regulated by a second less frequent cell population. When recombinant interleukin 2 is substituted for crude lymphocyte conditioned medium in these limiting dilution experiments, autocytotoxicity develops normally. Under these conditions, however, the autocytotoxic response is not down-regulated. Mixing crude lymphocyte-conditioned medium together with recombinant interleukin 2 restores the regulation of autocytotoxicity normally seen at high responder cell dose. These findings indicate that a second soluble factor present in the conditioned medium is necessary either for the activation, growth, or differentiation of the regulatory cell population or alternatively, to render the cytotoxic population responsive to the activity of regulatory cells. Gel filtration studies indicate that the molecular weight of this factor is between 60 and 80 kd. This factor appears to be distinct from known immunologically active cytokines. It is conceivable that deficiencies of this cytokine may be relevant to the pathogenesis of autoimmune diseases or graft-versus-host reactions.

Human neuroblastoma cells in culture: a model for neuronal cell differentiation and function.

The human neuroblastoma cell line, SH-SY5Y, differentiates into neuron-like cells according to morphological, biochemical and functional criteria when treated with biologically active phorbol-esters. The differentiated phenotype is described and alterations in proto-oncogene expression in connection with growth control and differentiation are presented and discussed.

Early activation of endogenous pp60src kinase activity during neuronal differentiation of cultured human neuroblastoma cells.

The proto-oncogene product pp60c-src is a tyrosine-specific kinase with a still unresolved cellular function. High levels of pp60c-src in neurons and the existence of a neuronal pp60c-src variant, pp60c-srcN, suggest participation in the progress or maintenance of the differentiated phenotype of neurons. We have previously reported that phorbol esters, e.g., 12-O-tetradecanoylphorbol-13-acetate (TPA), stimulate human SH-SY5Y neuroblastoma cells to neuronal differentiation, as monitored by morphological, biochemical, and functional differentiation markers. In this report, we describe activation of the pp60src (pp60c-src and pp60c-srcN) kinase activity observed at 6 h after induction of SH-SY5Y cells with TPA. This phenomenon coincides in time with neurite outgrowth, formation of growth cone-like structures, and an increase of GAP43 mRNA expression, which are the earliest indications of neuronal differentiation in these cells. The highest specific src kinase activity (a three- to fourfold increase 4 days after induction) was noted in cells treated with 16 nM TPA; this concentration is optimal for development of the TPA-induced neuronal phenotype. During differentiation, there was no alteration in the 1:1 ratio of pp60c-src to pp60c-srcN found in untreated SH-SY5Y cells. V8 protease and trypsin phosphopeptide mapping of pp60src from in vivo 32P-labeled cells showed that the overall phosphorylation of pp60src was higher in differentiated than in untreated cells, mainly because of an intense serine 12 phosphorylation. Tyrosine 416 phosphorylation was not detectable in either cell type, and no change during differentiation in tyrosine 527 phosphorylation was observed.

Analysis of three distinct Ly6-A-related cDNA sequences isolated from rat kidney.

Mouse Ly6A and Ly6C cDNA probes were hybridized to total RNA of rat tissues and, as in mouse, the highest level of Ly6-related transcripts was detected in kidney. Therefore, Ly6-related cDNA clones were isolated from a commercial rat kidney cDNA library in lambda gt11. Four of these (RK3, RK6, RK10, and RK11) have been fully characterized, and represent transcripts from three distinct genes. Each contains a reading frame encoding an amino acid sequence typical of the known Ly6 molecules: a 26aa leader (except in clone RK6 which has only two of its leader codons), followed by a sequence of 108 or 109aa containing 10 cysteines in excellent alignment with those of Ly6A. The three rat polypeptide sequences were more closely related to Ly6A than Ly6C, and more closely related to each other than to Ly6A. The most striking similarity between all these sequences is in the last 33aa at the C-terminal. Most of this is presumed to be cleaved off during post-translational addition of a phosphatidylinositol-glycan (PI-G) membrane anchor. Southern blot analysis of rat DNA probed with rat-Ly6 cDNA showed multiple band patterns indicative of a multigene family. No restriction fragment length polymorphism (RFLP) was evident amongst the six inbred rat strains tested. Anomalies in two of the rat cDNA clones, resulting from improper splicing of the original transcripts, correlated with Ly6Ca exon boundaries, thus suggesting conserved intron-exon organization.