Biomedical subjects

J R Frey

Publications and source records attributed to J R Frey.

At least 19 recordsLinked to original sources

PubMed2001

Proteomic analysis of rare molecular species of translated polypeptides from a mouse fetal thymus cDNA library.

Proteomic patterns from an ordered cDNA library of mouse fetal thymus origin of an overall complexity of 1536 clones are described. Patterns have been analyzed at 96, 12, or 8 clones in a mixture, or as individual clones. Clones yield in some instances a single spot, in other cases a complex cluster or family of spots is formed. The determination of the clonal address (a six-digit number, indicating the interception of three pooling dimensions) by inspection of pools of 8, 12 or 16 clones is a reliable approach; nevertheless a complete proof consists in retrieving the clone and then submitting to transcription, translation and proteomic analysis. The spot clusters are meaningful clone identifiers; cluster components (families of polypeptides) are characteristic of individual clones and are independent of clones coexisting (and being co-expressed) in a given pool. A 'cluster' originates from a single cloned message and might be due to post-translational modification (offered by the reticuleocyte machinery) or as a result of programmed degradation. Thirteen clones or families of clonal products are shown, and the heterogeneity of the 'appearance' of clones is documented. In about half, the assignment of a clonal polypeptide product to a storage well position has failed; this might be due to a variety of considerations elaborated herein. The arguments are presented, that analysis of abundant proteins of a cell (activated lymphocyte) comprises 'classical proteomics', but for the analysis of the rare molecular species of proteins, Poissonian approaches of replicable material have to be used.

Animals↗

PubMed2000

Increased protein synthesis after T cell activation in presence of cyclosporin A.

BACKGROUND: The immunosuppressive drug, cyclosporin A (CsA), blocks immune responses by inhibiting the calcineurin-dependent dephosphorylation of the nuclear factor of activated T cells (NFAT). We have previously reported that T cells activated in presence of CsA exhibit particular properties. In our study, we have tested the hypothesis that T cells activated in presence of CsA display a differential pattern of gene expression. METHODS: T lymphocytes were activated in vitro by Concanavalin A with or without CsA. The cells were: (1) pulsed with 35S-methionine to label the newly synthesized proteins that in turn were revealed by 2D-gel electrophoresis; (2) analyzed by flow cytometry for activation markers expression; and (3) examined by gel electrophoresis for early tyrosine phosphorylation events. RESULTS: The proteomic patterns of T lymphocytes activated by Concanavalin A, with or without CsA, were compared. In keeping with the well-known effect of the immunosuppressor, many polypeptides were not found in its presence. Remarkably, several newly synthesized polypeptides were detected only when activation was carried out in presence of CsA. In addition, immunologically relevant proteins, such as CD44 and CD69, escape CsA-inhibitory action. Furthermore, CsA did not modify the early protein tyrosine phosphorylation events resulting from T cell triggering. CONCLUSIONS: The present data show that the effect of CsA on protein synthesis is more complex than anticipated. Signaling provided by T cell activation and the blockade of the calcineurin-dependent pathway by CsA results in an altered program of gene expression.

Animals↗

PubMed2000

Global analysis of gene expression in cells of the immune system I. Analytical limitations in obtaining sequence information on polypeptides in two-dimensional gel spots.

We have outlined various aspects and limitations of the collective analysis of protein species of a cell (lymphocyte). We have indicated research directions that, in to our opinion, deserve more attention. We have evaluated mainly the approach used in our laboratory and we recognize that a bulk of important research on the interface of proteomics and genomics remains to be dealt with. It is of great value that we can proceed in our quest by trial and error. But as much as the human genome initiative was not implemented by trial and error, but by formulating new technological approaches, we hope that our approach can be incorporated in the mainstream of proteomics. We need several integrating research directions, some of which are outlined in this communication, namely the use of ordered cDNA libraries, cell-free expression systems, high density filter hybridization, identification of two-dimensional (2-D) gel spots in terms of their amino acid composition through biosynthetic labeling and identification of restriction sites in the corresponding coding sequences. In the accompanying paper the cDNA ordered library approach will be described in some detail.

B-Lymphocytes↗

PubMed2000

Global analysis of gene expression in cells of the immune system II. Cell-free translation products and high-density filter hybridization data.

We have developed an experimental system for linking information on cell-free transcription and translation products from cDNA clones with data obtained from hybridization signals from complex probes. The work described in this paper consists of two distinct processes, one being the construction of a system of clonal addresses and the other the identification of expressed genes involved in the studied processes. We describe the use of this system to identify genes involved in thymus development. Complex probes from fetal thymuses (GD15, 17 and newborn) of Balb/c mice were used to identify genes, which are up- or downregulated during the process of differentiation. The full set of information is available in the Clone-base of the Basel Institute for Immunology and will be retrievable from the website of the collaborating laboratories.

Animals↗

PubMed2000

Proteome analysis of activated murine B-lymphocytes.

Proteins extracted from murine B-lymphocytes after in vitro stimulation by lipopolysaccharide were separated by two-dimensional (2-D) polyacrylamide gel electrophoresis and analyzed by matrix assisted laser desorption/ionization mass spectrometry. Structural information on the protein entities from 153 spots was obtained. Since many of these spots occur as members of spot families, a smaller number --98 genes-- was found to be coding for the identified spots. The elucidated proteins belong to groups of functional categories; we found 26 enzymes, 36 regulatory proteins, 15 chaperones, 15 structural proteins, 4 immunoglobulins, 1 ribosomal and 1 histone protein. A comparison between expected and observed molecular masses yields a good correlation for the majority of the compared spot entities. This set of proteins now identified in the context of a lymphocyte 2-D gel pattern should advance further studies on lymphocyte functions.

Animals↗

PubMed1997

Neutrophils as a source of putative restriction proteases: degradation of mammalian and yeast proteins monitored by two-dimensional gel electrophoresis.

We have compared the ability of intact neutrophils to degrade a complex substrate of proteins from mammalian and yeast origin. The substrate was obtained by biosynthetic labeling, and subsequent lysis of K562 cells (leukemic cell line) and of yeast culture. The mammalian substrate consisted of 619 and the yeast substrate of 185 different polypeptides, as visualized and represented on two-dimensional gel patterns. Upon incubation of the mammalian substrate with neutrophils, the bulk of spots disappeared so rapidly that after 240 min of incubation only 21 spots were detectable. Just one spot remained unaltered in its intensity throughout the whole period of incubation. About 440 spots reveal a t1/2 shorter than 8 min. Yeast substrate is represented by a smaller number of the starting polypeptides (185) from which 55 spots "survive" the neutrophil treatment. About 30 spots have a t1/2 shorter than 8 min. We conclude that neutrophils are equipped with a potent proteolytic apparatus, and this is capable of eliminating various proteins in a highly efficient manner. The system is much less effective in eliminating proteins from distant species, like yeast. Although the cells governing and regulating the immune system are clearly of lymphoid origin, it might well be that the preimmune task of eliminating self antigens in a manner as predicted in the restriction protease hypothesis is performed by neutrophils.

Animals↗

PubMed1997

Restriction sites as identification tags for lymphocyte cDNAs.

A cDNA library was prepared from BW 5147 murine lymphoma cells in lambda ecc III phage and randomly partitioned into 291 sectors, each with 800-1000 recombinant phage plaques. One sector was chosen for further characterization in terms of sensitivity to restriction endonuclease cutting. Aliquots of DNA preparations from this sector were treated with XhoI, SmaI, NcoI, PvuII, PstI, HindIII, EcoRI, BamHI, and ApaLI before being used as templates in a cell-free expression system. The polypeptide products were separated by two-dimensional (2-D) gel electrophoresis and radiofluorographs of the gels were submitted to computer-aided image analysis. The matched patterns were inspected for the presence or absence of spots upon individual endonuclease treatments. Thereafter the results were integrated in a data matrix which served as a basis to construct "restriction tags" for all spots. These (restriction) tags are binary numbers termed "cut numbers" and are a representation of the set of recognition sequences which are (or are not) part of the coding sequence. From 493 sequences (visualized as 2-D gel spots), 12 were not cut by any of the nine enzymes, while 45 were cut by all of them. The percentages of sequences resistant to enzyme treatment ranged between 17% and 77% for NcoI and XhoI, respectively. The enzyme treatments led to the appearance of a certain portion of "new spots", probably products from truncated sequences. From 512 possible cut numbers, 136 were assigned to the 493 spots. Restriction tags are available to facilitate retrieval of cDNA clones from the (partitioned) cDNA library.

Animals↗

PubMed1997

Analysis of a randomly assorted cDNA library from BW 5147 lymphoid cells. Frequency estimates based on computer aided concatenation matching of 2D gel polypeptide products.

A cDNA library was divided into 291 sectors of low complexity, 800-1000 recombinant phage plaques per sector. Aliquots of DNA from sectors prepared from high titer phage were subjected to in vitro transcription using T7 polymerase and thereafter RNA was translated in a cell-free rabbit reticulocyte system in the presence of [35S] methionine. The resulting polypeptides were separated by 2D gel electrophoresis. Radiofluorographs of the gels prepared from 10 sectors were subjected to scanning and image analysis. A multilevel spot matching procedure was employed allowing us to recognise spot occurrence in the 10 sectors. The number of detected polypeptide spots per sector varied between 147 and 325. Overall, 1082 different spots were counted totalling 1983 spots considering multiple entries. The distribution of the spots and the frequency distribution of the RNA population among the 10 sectors are shown. The highest detected frequency is 10(-2), while one half of the RNA molecular species are present at a frequency of 10(-3) or lower.

Animals↗

PubMed1996

Protein expression during murine thymus differentiation.

Driven by our long-standing interest in identifying proteins of the immune system and in characterizing processes involved in lymphocyte differentiation, we studied protein expression in biosynthetically labeled fetal and newborn thymus by 2D gel electrophoresis. Autoradiographs of the gels were scanned with a densitometer and image analysis was performed using the Kepler system. Calibrated polypeptide spot abundances (volumes) were compared to assesses qualitative and quantitative changes of the spot volumes. Among over 300 proteins evaluated at GD (gestation day) 13, 15, and 17, there were sets of proteins that increased and other that decreased in intensity. We could in addition recognize proteins that were completely absent at GD 13 and/or 15 and that appeared thereafter to gradually increase in intensity. Conversely, various polypeptide spots present at early stages (at GD 13 and 15) disappear later (at GD17 or at birth). Among the proteins that increase in intensity prevail molecules with masses less than 35 kD, whereas a considerable portion of those that decrease in intensity are characterized by masses above 60 kD. Spots reported in this communication were not defined beyond tagging them with numbers, which is a prerequisite to follow them up in the proteinpaedia developed in our laboratory. The next step will be to retrieve the coding sequences from the existing partitioned cDNA library (BW 5147) as well as from thymocyte subtraction libraries. We predict that among those polypeptides with varying intensity, important regulatory proteins in thymus development will be found.

Animals↗

PubMed1995

Human lymphocyte cDNA ordered library analyzed by 2D gel electrophoresis. 1. Pooling strategy and matching of gel patterns.

We have analyzed an ordered library of 4,608 cDNA clones from the CEM human leukemic cell line. The aim was to facilitate gene retrieval, to enable immediate access to cDNA clones and to provide information on the protein expression of the individual clones in a 2D gel readout. The matrix array of 24 x 16 x 12, each position of which contained lambda jacII phage from one plaque, enabled us to establish pools of clones along the three axes (24 pools of complexity 192 cloned entities, 16 pools of complexity 288 and 12 pools of complexity 384). The total cDNA complexity is here reduced to such a level that spots which in more complex gels served as landmark spots are not present in each pool, and thus cannot serve as landmarks anymore. The image analysis of such gels and especially the matching of spots is not reliable under these circumstances. In order to achieve reliable matching, additional samples were created, such that pools were co-electrophoresed according to a special concatenation scheme; these samples then contained over-lapping elements (e.g., pools 1 + 2 + 3 and 3 + 4 + 5 have at least those spots in common, which originate from pool 3). This approach turned out to be feasible and we have completed the matching of one half of the ordered library. Already from the present stage of analysis we have obtained valuable information on the cDNA library and on the distribution of clones in this library.

DNA, Complementary↗

PubMed1995

Human lymphocyte cDNA ordered library analyzed by 2D gel electrophoresis. 2. Frequency distribution of mRNA populations.

Cell-free transcription and translation products from an ordered library of cDNA clones from the CEM human leukemic cell line were submitted to analysis using two-dimensional gel electrophoresis as a read out system. The matrix array of 24 x 16 x 12 wells contained in each of the positions lambda jacII phages from one plaque. Pools of clones along the three axes (24 x-pools, 16 y-pools and 12 z-pools) were established. Results obtained upon matching of 12 x-pools were scrutinized for estimating the frequency of cDNA molecular species in the library. The results obtained are interpreted in such a way that there are no discrete distributions of mRNA molecular species, but rather there is a continuous distribution of mRNA's covering a wide range of frequencies. The lowest frequency found was about 4.5 x 10(-4) and the highest 1.6 x 10(-2). About half of all clones can be found among these low frequency ones (each occurring 0.45 times among 1,000 clones).

Cell-Free System↗

PubMed1994

The amino acid composition of 350 lymphocyte proteins.

We determined the amino acid composition of proteins of Sp2 hybridoma cells by a procedure which assembles the information on the polypeptides upon two-dimensional gel electrophoresis, such that biosynthetic labeling with 20 different 3H amino acids provides the data--spot intensities--on the relative representation of the detected polypeptides. The gels were impregnated with 2,5-diphenyloxazol (PPO) and suitably exposed radiofluorographs were selected for analysis. The images originating from the 12 cultures labeled with amino acids R, A, H, I, L, K, M, F, P, S, T and Y were analysed with the Kepler image analysis system. The spot volume data of the 12 analysed patterns were corrected for the unequal labeling efficiencies of the 3H amino acids and for the various exposure times. This correction is performed by applying calibration factors based on the amino acid determination of a hydrolysate of the analysed cells. After the calibration step was applied to the data files we used the amino acid compositions of nine proteins taken from a database to establish for each of these proteins the correlation coefficients with the image analysis derived amino acid compositions of all spots. The correlation coefficients allow us to tentatively identify polypeptide spots on two-dimensional gels, while the amino acid composition of 350 investigated two-dimensional gel spots is usable as an identification tag in the gene retrieval from our cDNA libraries.

Amino Acids↗

PubMed1993

Restriction sites as identification tags for the gene catalog: a 2D gel model.

In our effort to collect, organize and assemble data from lymphocyte cDNA libraries, we assign DNA restriction sites collectively to the spots on two-dimensional (2D) gel patterns. In order to test the efficiency and reliability of such an approach, we have modeled the restriction analysis of cDNA libraries with a panel of restriction endonucleases. The work has two parts. In the first, we have chosen 255 proteins from the EMBL data base and determined whether or not their coding sequences contain restriction sites for the enzymes of our choice. In order to apply a sufficient discriminatory power we decided to use a relatively large number of cleaving enzymes with low and high cutting frequencies. In total, 13 restriction enzymes were chosen, which could distinguish 2(13) or 8192 different restriction site combinations. We have compiled a table in which the absence or presence of restriction sites yields a pattern of 'zeros' and 'ones'. Such a restriction pattern can be read as a binary number. The binary numbers with maximally 13 digits would uniquely assign each of the 255 proteins if the nucleotide sequences would be truly at random. As the restriction sites are not randomly distributed, the 'typing' does not yield a unique assignment. The choice of sequences was not random either. In fact, there are some human nucleotide sequences which possess the same cut number (the decimal equivalent of the binary number representing the restriction pattern). In spite of this redundancy, 141 coding sequences could uniquely be distinguished by the above treatment. In the second part of the project we have used the above mentioned coding sequences to prepare two-dimensional maps (plots of charge vs size) of the same kind as one obtains from experimental 2D gels and submitted such a map together with 13 maps of restriction enzyme treated populations to a computer image analysis. Ideally, one would expect results (cut numbers) congruent to those obtained in the first part of the work. In the modeled system we were confronted with 2D maps which closely resembled the experimental situation (e.g. some spots were close together and overlapping) and instances of incorrect spot detection yielding 'false cut numbers'. From 255 proteins we were able to assign unequivocally 161 proteins. To implement the model in an actual experiment we will perform the digestion with the restriction enzymes in duplicate, and only spots assigned the same cut number upon the two independent treatments will be considered as carrying a valid restriction tag.

Base Sequence↗

PubMed1992

Thymus-grafted SCID mice show transient thymopoiesis and limited depletion of V beta 11+ T cells.

To seek direct evidence for the notion that stem cells in the thymus need to be constantly replenished from the bone marrow (BM), fetal (day 15) thymuses from normal BALB/c mice were grafted into T and B cell-deficient C.B-17 SCID mice (both H-2d, I-E+). The thymus grafts in these mice showed normal thymopoiesis for the first 3 wk postgrafting but then developed sudden atrophy with near complete loss of CD4+8+ cells by 4-5 wk. Such atrophy was not seen when the thymus-grafted mice were cotransplanted with normal BM cells. The lymph nodes of SCID mice receiving thymus grafts alone contained mature T cells but virtually no B cells. This lack of B cells was associated with aberrant I-E-restricted V beta deletion: the depletion of V beta 3+ and V beta 5+ T cells was near complete, whereas V beta 11+ cells showed only marginal depletion.

Animals↗

PubMed1992

Inhibition of proliferation by retinoids, cytokines and their combination in four human transformed epithelial cell lines.

Various combinations of retinoids and cytokines were examined for their synergistic effect on inhibition in proliferation of four human transformed epithelial cell lines, MCF7 (mammary carcinoma), SCC4, SCC15 and A431 (squamous cell carcinomas). Synergism depended on the cell line tested, to some degree on the specific retinoid but particularly on the type of cytokine used. IFN alpha had the widest spectrum of activity. IFN gamma, TNF-alpha, IL-1, EGF and TGF-beta also exerted a synergistic effect on proliferation inhibition in certain cell lines, whereas G-CSF was inactive. Association of retinoids and cytokines represents a new approach to antitumor chemotherapy.

Breast Neoplasms↗

PubMed1991

Antiproliferative activity of retinoids, interferon alpha and their combination in five human transformed cell lines.

Tretinoin, isotretinoin and acitretin were examined for their capacity to modulate the proliferation of the cell lines: HL-60 (acute promyelocytic leukemia), MCF7 (mammary carcinoma), SCC4, SCC15 and A431 (squamous cell carcinomas). Retinoids inhibited proliferation to a varying extent in all 5 cell lines. The cytokine IFN alpha had a significant antiproliferative effect only on HL-60, SCC4 and SCC15. The combination of retinoids with IFN alpha led in all 5 cell lines to a more profound reduction in proliferation than either retinoids or IFN alpha alone.

Acitretin↗

PubMed1991

Efficient purification of recombinant human tumor necrosis factor beta from Escherichia coli yields biologically active protein with a trimeric structure that binds to both tumor necrosis factor receptors.

A fast and efficient method for medium scale purification of recombinant human tumor necrosis factor beta (rTNF-beta) from Escherichia coli cells is described. The purified rTNF-beta displayed biological activity similar to rTNF-alpha in a WEHI 164 cell cytotoxicity assay. The titration curve of rTNF-beta and elution profiles of rTNF-beta in gel filtration experiments were different from those of rTNF-alpha. However, light scattering and ultra-centrifugation studies showed that both cytokines have trimeric structures in solution at 0.5 mg/ml, with minor differences in the distribution of nontrimeric species. rTNF-beta bound to purified 55- and 75-kDa TNF receptors with high affinity. The binding of rTNF-beta to either receptor was analyzed on Scatchard plots and compared with that of rTNF-alpha.

Binding, Competitive↗

PubMed1991

The principal tumor necrosis factor receptor in monocyte cytotoxicity is on the effector cell, not on the target cell.

Several tumor target cell lines, prototypically K562 cells, are resistant to lysis by recombinant tumor necrosis factor (TNF alpha) but are killed by monocytes expressing membrane-associated TNF, suggesting that membrane TNF could account for monocyte-mediated cytotoxicity. Formaldehyde-fixed monocytes or extracted monocyte membrane fragments are cytotoxic to K562 target cells. Treatment of monocytes with interferon-gamma (IFN-gamma) increases cytotoxicity by live and fixed cells or by extracted monocyte membranes. Both TNF and TNF receptors are detectable on monocyte membranes by FACS analysis, and the levels of each are modulated by treatment with IFN-gamma. Cytotoxicity can be inhibited by either anti-TNF or anti-TNF receptor antibodies. Incubation of effector cells with exogenous soluble TNF prior to fixation or membrane preparation increases their cytotoxicity. In contrast, incubation of the target cells with exogenous TNF neither increases nor decreases killing by effector cell membrane fragments or intact effector cells. The data suggest that the TNF receptors on the effector cell, but not on the target cell, play a crucial role in TNF-mediated cytotoxicity.

Cytotoxicity, Immunologic↗