Proteome analysis of nuclear matrix proteins during apoptotic chromatin condensation.

The nuclear matrix (NM) is considered a proteinaceous scaffold spatially organizing the interphase nucleus, the integrity of which is affected during apoptosis. Caspase-mediated degradation of NM proteins, such as nuclear lamins, precedes apoptotic chromatin condensation (ACC). Nevertheless, other NM proteins remain unaffected, which most likely maintain a remaining nuclear structure devoid of chromatin. We, therefore, screened various types of apoptotic cells for changes of the nuclear matrix proteome during the process of apoptotic ACC. Expectedly, we observed fundamental alterations of known chromatin-associated proteins, comprising both degradation and translocation to the cytosol. Importantly, a consistent set of abundant NM proteins, some (e.g. hNMP 200) of which displaying structural features, remained unaffected during apoptosis and might therefore represent constituents of an elementary scaffold. In addition, proteins involved in DNA replication and DNA repair were found accumulated in the NM fraction before cells became irreversibly committed to ACC, a time point characterized in detail by inhibitor studies with orthovanadate. In general, protein alterations of a consistent set of NM proteins (67 of which were identified), were reproducibly detectable in Fas-induced Jurkat cells, in UV-light treated U937 cells and also in staurosporine-treated HeLa cells. Our data indicate that substantial alterations of proteins linking chromatin to an elementary nuclear protein scaffold might play an intriguing role for the process of ACC.

Elevated plasma levels of crosslinked fibrinogen gamma-chain dimer indicate cancer-related fibrin deposition and fibrinolysis.

Cancer-related fibrin deposition and fibrinolysis were investigated by two-dimensional gel electrophoresis of human solid tumor and effusion specimen in addition to plasma samples. Fibrinogen gamma-chain dimer indicating fibrin deposition and plasmin-generated fibrinogen beta-chain fragments were identified in various solid tumor types by amino acid sequencing, mass spectrometry analysis and Western blotting. In tumor-associated effusions, these techniques allowed to observe plasmin-generated fragments of fibrinogen alpha, beta and gamma-chains in addition to elevated levels of acute-phase proteins. Similar observations were made in case of inflammation-associated effusions. No fibrin degradation product was observed in plasma samples, however, high amounts of fibrinogen gamma-chain dimer crosslinked by transglutaminase were detected in plasma from tumor patients, but not in plasma from controls and patients suffering acute infections and/or inflammations. This finding demonstrated that high transglutaminase activity may be associated with cancer. The presented data indicate that the amount of crosslinked fibrinogen gamma-chain dimer in plasma may correlate with tumor-associated fibrin deposition. The tumor-biological relevance of this potential marker protein is discussed.

hNMP 200: a novel human common nuclear matrix protein combining structural and regulatory functions.

Previously we have reported about human nuclear matrix proteins (hNMPs) with increased reassembling and potential filament-forming capability [C. Gerner et al., 1999, J. Cell. Biochem. 74, 145-151]. Here, we cloned the cDNA of one of these proteins, hNMP 200, following partial amino acid sequencing of the novel 56-kDa nuclear protein. Sequence alignments show hNMP 200-related proteins in metazoans, plants, and yeast, the homologous Saccharomyces cerevisiae protein prp19 being an accessory, but essential, factor for pre-mRNA processing. Evidence for any enzymatic activity was not detected. However, the hNMP 200 primary sequence contained five consensus WD-repeat sequences, indicative of participation and regulatory function in larger protein assemblies. Northern blot analysis and 2D protein electrophoresis showed ubiquitous expression of hNMP 200 in a variety of cell types. (35)S labeling studies indicated a high metabolic stability of the protein. The hNMP 200 gene was assigned to chromosomal region 11q12.2. Confocal laser scanning microscopy revealed that the intracellular localization conformed with that reported for other structural nuclear proteins. In interphase cells, green fluorescent protein-tagged hNMP 200 was predominantly nucleoplasmic. Structures with speckled appearance extended through several sections of in situ-isolated nuclear matrices. During cell division hNMP 200 became irregularly distributed in prophase, sparing regions of condensing chromatin. In anaphase it was concentrated in the spindle midzone. The putative dual function of the novel NMP is discussed. Being a component of the nuclear framework, it may provide structural support for components of the RNA-processing machinery, thereby also modulating splicing activities.

Differential nuclear localization and nuclear matrix association of the splicing factors PSF and PTB.

A monoclonal antibody raised against nuclear matrix proteins detected a protein of basic pI in human nuclear matrix protein samples of various cellular origin. The ubiquitously occurring (common) nuclear matrix protein was identified as splicing factor PSF (PTB associated splicing factor). The interaction between the splicing factors PSF and PTB/hnRNP I was confirmed by co-immunoprecipitation from nuclear salt extracts. However, the nuclear localization of PSF and PTB and their distribution in subnuclear fractions differed markedly. Isolated nuclear matrices contained the bulk of PSF, but only minor amounts of PTB. In confocal microscopy both proteins appeared in speckles, the majority of which did not co-localize. Removing a large fraction of the soluble PTB structures by salt extraction revealed some colocalization of the more stable PTB fraction with PSF. These PTB/PSF complexes as well as the observed PSF-PTB interaction may reflect the previously reported presence of PTB and PSF in spliceosomal complexes during RNA processing. The present data, however, point to different cellular distribution and nuclear matrix association of the majority of PSF and PTB.

Nuclear matrix proteins specific for subtypes of human hematopoietic cells.

Nuclear matrices were prepared from isolated subtypes of human hematopoietic cells and from cultured leukemia cells. The nuclear matrix proteins were analyzed by high-resolution two-dimensional gel electrophoresis and computer-assisted image analysis. While more than 200 protein spots were shared among the cells, about 50 distinct spots were found characteristic for individual cells or groups of related cells. This allowed to differentiate between hematopoietic cells and nonhematopoietic cells, lymphocytes and myeloid cells, monocytes, neutrophils, and promyelocytic leukemia cells. B and T lymphocytes could not be differentiated. Myeloid cells with their polymorph nuclei were characterized by the presence of 13 and by the absence of seven distinct spots, as well as by low concentrations of nuclear lamins and of heterogeneous nuclear ribonucleoproteins. Neutrophils with multilobular nuclei displayed six additional spots, while lacking 18 nuclear matrix protein spots. The nuclear matrix of proliferating cells showed three distinct spots in addition to proliferating cell nuclear antigen, increased concentrations of numatrin (B23), and heterogeneous nuclear ribonucleoproteins. The described cell-specific nuclear matrix proteins may represent new markers for hematopoietic cells.

Identification and characterization of the ubiquitously occurring nuclear matrix protein NMP 238.

By systematic comparison of two-dimensional electrophoretic patterns of nuclear matrix proteins an ubiquitously occurring (common) nuclear matrix protein, termed NMP 238, was detected. Localization of the protein in isolated nuclear matrices and in nuclear and cytoplasmic regions of cells was determined by confocal immunofluorescence microscopy. N-terminal protein sequencing, mass spectrometry, and sequencing of a human EST cDNA clone showed identity of the protein with a nuclear protein, termed TIP49, of as yet uncertain function. Expression of the corresponding gene in diverse human and rat cells was confirmed by Northern blotting. The protein displays two nuclear localization signals. Sequence homologies indicate evolutionary related proteins in nematodes, yeast, and archaebacteria. Similarities to the AAA family of proteins and to a subgroup of chaperones suggest that the nuclear matrix protein may play a role in the assembly and ATP-dependent anchorage of proteins.

Similarity between nuclear matrix proteins of various cells revealed by an improved isolation method.

Comparative analysis of nuclear matrix proteins by two-dimensional electrophoresis may be greatly impaired by copurifying cytoskeletal proteins. The present data show that the bulk of adhering cytofilaments may mechanically be removed by shearing of nuclei pretreated with vanadyl ribonucleoside complexes. Potential mechanisms of action not based on ribonuclease inhibition are discussed. To individually preserve the integrity of nuclear structures, we developed protocols for the preparation of nuclear matrices from three categories of cells, namely leukocytes, cultured cells, and tissue cells. As exemplified with material from human lymphocytes, cultured amniotic cells, and liver tissue cells, the resulting patterns of nuclear matrix proteins appeared quite similar. Approximately 300 spots were shared among the cell types. Forty-nine of these were identified, 21 comprising heterogeneous nuclear ribonucleoproteins. Heterogeneous nuclear ribonucleoproteins L and nuclear lamin B2 isoforms were identified by amino acid sequencing and mass spectrometry. However, individually expressed proteins, such as the proliferating cell nuclear antigen, also pertained following application of the protocols. Thus, enhanced resolution and comparability of proteins improve systematic analyses of nuclear matrix proteins from various cellular sources.

A novel spliced transcript of human CLAPS2 encoding a protein alternative to clathrin adaptor protein AP17.

Transcripts of genes encoding proteins of clathrin complexes have been reported to undergo tissue-specific alternative splicing. AP17, encoded by human CLAPS2 cDNA, is the small chain of the major clathrin adaptor complex AP-2 associated with mammalian plasma membranes. In this study, two cDNAs were isolated from a cDNA library of human blood cells. Whereas one cDNA encoded AP17, the other cDNA encoded a putative novel protein variant, termed AP17Delta. Both coding regions were completely sequenced. Consisting of 142aa residues, the predicted protein AP17Delta of 12kDa lacks 38aa residues of AP17. Using specific primers for RT-PCR, mRNAs for AP17Delta and AP17 were found in leukocytes and cultured leukemia cells. The finding of a putative intron in a human EST cDNA clone suggests that mRNAs for AP17 and AP17Delta are formed by alternative splicing. In addition, the identity of human and rat AP17 amino acid sequences is demonstrated.

The use of biotinylated poly(ADP-ribose) for studies on poly(ADP-ribose)-protein interaction.

Poly(ADP-ribose) is routinely detected by the use of radioactive polymers formed from labeled substrates. In this report a simple and time-saving method for the biotinylation and the detection of poly(ADP-ribose) on blots is described. The polymer modified by light-induced reaction with photobiotin was colorimetrically detected and quantified, using streptavidine-alkaline phosphatase conjugates. The separation of poly(ADP-ribose) chains on polyacrylamide gels was not affected by the biotinylation of the polymers. When biotinylated poly(ADP-ribose) was used to detect the poly(ADP-ribose) binding capability of proteins in ligand blots, the results were comparable to those obtained with poly([32P]ADP-ribose). Experiments with histones and rat liver nuclear proteins demonstrate that in studies on poly(ADP-ribose)-protein interaction, this method is applicable to the detection of poly(ADP-ribose) binding proteins.

Nucleolar proteins B23 and C23 as target antigens in chronic graft-versus-host disease.

Previously we observed that sera from recipients of allogeneic bone marrow transplants who developed extensive chronic graft-versus-host disease (GVHD) intensively stained the nucleolar region of target cells in indirect immunofluorescence microscopy. To identify the target antigens, immunoblotting experiments were performed using isolated nuclei, isolated nucleoli, and purified nuclear and nucleolar proteins as the antigen source. The nucleolar phosphoproteins B23 and C23 were identified as the main target antigens. Eleven of 19 extensive chronic GVHD sera reacted with these nucleolar phosphoproteins. In addition, four sera recognized histone H1, and two sera recognized the nuclear lamins A and C. Our patients reacting with the nucleolar proteins had symptoms resembling that of scleroderma or Sjögren's syndrome.

Autoantibodies in chronic GVHD: high prevalence of antinucleolar antibodies.

Sera from 32 bone marrow allograft recipients were screened for the presence of autoantibodies 4-61 months post-graft. Sera from 12 of 19 patients with extensive chronic graft-versus-host disease (c-GVHD) stained the nucleolar region strongly in immunofluorescence, indicating the presence of specific antinucleolar antibodies. In contrast, none of three patients with limited and none of 10 patients without c-GVHD had antinucleolar antibodies. Antibodies reacting with nuclear constituents other than nucleoli were found in five of the 12 antinucleolar positive patients. The appearance of antinucleolar antibodies coincided with early clinical symptoms of c-GVHD. We conclude that the appearance of antinucleolar antibodies after bone marrow transplantation is specific for patients with extensive c-GVHD. Furthermore, the development of extensive c-GVHD is paralleled by the emergence of these antinucleolar antibodies.

Identification of ADP-ribosylated histones by the combined use of high-performance liquid chromatography and electrophoresis.

Reversed-phase high-performance liquid chromatography (HPLC) was employed for analysing mono- and oligo(ADP-ribosyl)ated histones. Under the chromatographic conditions described, the ADP-ribosylated histones showed similar retention times to the unmodified histones, although the molecular weight and the charge of the proteins are significantly altered by their modification. The simultaneous elution of unmodified and labelled modified histones was detected by two types of gel electrophoresis and by autoradiography. In addition, the HPLC fractions did not display overlapping ladders of the multiply modified histones, as is commonly seen in one-dimensional electrophoretic analyses of unfractionated material. Hence individual bands could be unambiguously assigned. After in vitro labelling of isolated rat liver nuclei, the following ADP-ribosylated and unmodified histones were identified by HPLC and gel electrophoresis: histone H1(0), four histone H1 subfractions, histone H2A.1, histone H2A.2, oxidized histone H2A.2, histone H2A.X, histone H2A.Z, histone H2B, three histone H3 variants and histone H4.

The effect of poly(ADP-ribose) on interactions of DNA with histones H1, H3 and H4.

The competition between poly(ADP-ribose) and DNA for binding of the histones H1, H3 and H4 was studied, using a membrane filter-binding test. Poly(ADP-ribose) differently affected the interaction between DNA and the individual histones. While poly(ADP-ribose) effectively competed with DNA for binding of histone H4, it equally competed with DNA for binding of histone H3 and only inefficiently competed with DNA for binding of histone H1. Moreover, preformed complexes were correspondingly affected by the addition of competing polynucleotides, thereby also indicating the reversibility of complex formation. The competition capacity of DNA for histone H4 binding did not depend on DNA size. Competition experiments with poly(A) also indicated that poly(ADP-ribose) preferentially affected DNA-histone H4 interaction. The significance of the differing binding properties is discussed with regard to the possible molecular function of poly(ADP-ribose), especially with regard to its potential effect on nucleosome structure.

Fibronectin observed in the nuclear matrix of HeLa tumour cells.

We have investigated the intracellular distribution of insoluble fibronectin in HeLa tumour cells. By indirect immunofluorescence microscopy fibronectin was detected in the nuclear region, but not in the region of the cell surface. Isolated nuclei and isolated nuclear matrices also stained for fibronectin. By quantitative enzyme-linked immunosorbent assay (ELISA), fibronectin was found almost exclusively in the subcellular fraction of isolated nuclear matrices. Using immunoblotting techniques fibronectin was detected in nuclear matrices isolated from cells grown in standard and in fibronectin-depleted medium. The data demonstrate that fibronectin in HeLa tumour cells is preferentially associated with the nuclear matrix.

Poly(ADP-ribose) effectively competes with DNA for histone H4 binding.

The effect of poly(ADP-ribose) on DNA-histone H4 interaction was studied using a nitrocellulose filter binding assay. Poly-(ADP-ribose) was found to form poly(ADP-ribose)-histone H4 complexes at physiological salt concentrations. The homopolymer effectively competed with DNA for histone H4 binding. Poly(ADP-ribose) was also capable of displacing DNA from preformed DNA-histone H4 complexes. Our hypothesis is that poly(ADP-ribose), locally and transiently formed at the site of DNA damage, causes dissociation of DNA from the nucleosome particle or nucleosome unfolding.

Modification of nuclear matrix proteins by ADP-ribosylation. Association of nuclear ADP-ribosyltransferase with the nuclear matrix.

Nuclear matrices were isolated by treatment of isolated HeLa cell nuclei with high DNase I, pancreatic RNase and salt concentrations. ADP-ribosylated nuclear matrix proteins were identified by electrophoresis, blotting and autoradiography. In one experimental approach nuclear matrix proteins were labeled by exposure of permeabilized cells to the labeled precursor [32P]NAD. Alternatively, the cellular proteins were prelabeled with [35S]methionine and the ADP-ribosylated nuclear matrix proteins separated by aminophenyl boronate column chromatography. By both methods bands of modified proteins, though with differing intensities, were detected at 41, 43, 46, 51, 60, 64, 69, 73, 116, 140, 220 and 300 kDa. Approximately 2% of the total nuclear ADP-ribosyltransferase activity, but only 0.07% of the nuclear DNA, was tightly associated with the isolated nuclear matrix. The matrix-associated enzyme catalyzes the incorporation of [32P]ADP-ribose into acid-insoluble products of molecular mass 116 kDa and above, in a 3-aminobenzamide-inhibited, time-dependent reaction. The possible function of ADP-ribosylation of nuclear matrix proteins and of the attachment of ADP-ribosyltransferase to the nuclear matrix in the regulation of matrix-associated biochemical processes is discussed.

Transport of beta-globin mRNA from nuclei of murine Friend erythroleukemia cells. Reversible inhibition of transport by the oxidizing sulfhydryl reagent o-iodosobenzoate.

An in vitro assay system for analysis of beta-globin mRNA transport is described. Nuclei isolated from murine Friend erythroleukemia cells induced to synthesize globin mRNA, were incubated in micro-assays. By electrophoresis and hybridization analysis, released 9-S beta-globin mRNA was shown to be undegraded. After direct blotting, the released mRNA was quantified by hybridization with a labeled plasmid containing a beta-globin DNA restriction fragment. The inducibility of beta-globin mRNA transport corresponded to that previously reported for the release of rapidly labeled RNA in other assay systems. In contrast to the ineffectiveness of high concentrations of the sulfhydryl reagent iodoacetate, low concentrations of the oxidizing sulfhydryl reagent, o-iodosobenzoate, inhibited the release of beta-globin mRNA from nuclei of erythroleukemia cells, as well as the release of rapidly labeled RNA from rat liver nuclei. The inhibitory effect of the oxidizing agent on beta-globin mRNA transport could be reversed by postincubation of the nuclei with the reducing agent, dithiothreitol. The potential role of disulfide bond formation on RNA transport is discussed.

Enzyme activities in human breast tumor cells and sera.

Galactosyltransferase (GalTF), sialyltransferase (SiaTF), fucosyltransferase (FucTF), 5'-nucleotidase (5'Nucl), and ADP-ribosyltransferase (RibTF) were determined in three subcellular fractions of tumor cells and adjacent control tissue from 20 patients with small primary infiltrating ductal adenocarcinomas of the breast. Viable, as pure tumor cell populations as possible were isolated, subfractionated, and their enzyme levels compared to those in the patients' sera. The activities in tumor cells of the three glycosyltransferases were two- to seven-fold higher, whereas 5'-Nucl and RibTF showed reduced activities when compared to adjacent noninvolved tissue. Serum GalTF and SiaTF were slightly elevated in early mammary carcinoma, whereas FucTF, 5'Nucl, and RibTF were decreased in comparison with a control group. The proposed tumor origin of circulating enzymes could not be confirmed. Surprisingly, only for RibTF could a correlation between tumor and serum activity be established; a weak correlation was found for SiaTF. However, no such relationship could be determined for GalTF, FucTF, or 5'Nucl. In conclusion, the enzyme profile of the tumor cell does not, except for RibTF, appear in the serum. Serum enzyme profiles, therefore, do not permit detection of the early stages of breast cancer. A high correlation between RibTF activity and cytosol estrogen and progesterone receptor levels has been determined in tumor cells, possibly indicating slower growing, more differentiated types of breast tumors.

Predominance of a cell population less sensitive to carcinogenesis in neoplastic cells of 3-methylcholanthrene-induced tumors in mouse aggregation chimeras.

Tumors were induced by i.m. injections of 3-methylcholanthrene (0.5 mg) in 100% experimental aggregation chimeras derived from two mouse strains C57Bl/6J (hereafter called B6) and A/J, dimorphic for the enzyme glucosephosphate isomerase (Gpi-1a or Gpi-1b) and differing in coat color, aryl hydrocarbon hydroxylase inducibility, and cytotoxic activities of natural killer cells and macrophages. In the majority of host tissues and organs, such as coat, lung, spleen, and skeletal muscle, the B6 phenotype was predominant. Likewise, the nonneoplastic intratumoral host cells of both induced primary tumors and parental tumor transplants in chimeras were of B6 origin. In contrast, neoplastic cells in 70% of the tumors originated exclusively from the less aryl hydrocarbon hydroxylase-inducible and less immune competent A/J strain. The A/J origin was verified by subsequent cell culturing of the tumors. Only 30% of the tumors contained neoplastic cells of both A/J and B6 phenotype. A further reduction of mixed tumors was achieved with lower doses (0.1 and 0.06 mg) of the carcinogen. The dominance of the A/J phenotype of the tumors contrasted not only with aryl hydrocarbon hydroxylase inducibility and host cell composition but also with tumor pathogenesis (at 0.5 mg 3-methylcholanthrene) in the parental strain. Whereas tumor incidence was 100% in the B6 strain, it was only 65% in A/J mice, with tumors also developing later. As the in vivo and in vitro growth rates of parental strain-derived tumors were comparable, a cell selection caused by different growth rates favoring the A/J phenotype appeared unlikely.

[The value of poly-C-specific serum ribonuclease and CEA in the diagnosis of pancreatic carcinoma (author's transl)]. / Zur Anwendbarkeit der Poly-C-spezifischen Serum Ribonuklease und des CEA in der Diagnose des Pankreaskarzinoms.

The possible role of poly(C)RNase serum activity and CEA serum level for early detection and differentiation of pancreatic carcinoma and its specificity and valuability were critically analyzed: Serum RNase (median, min-max) with polycytidin as substrate was determined in 13 "normal" patients (14.6 E/ml, 4.3--29.8 E/ml), 16 patients with pancreatic cancer (T3 or metastases) (17.6 E/ml, 6--49-9 E/ml), 15 patients with chronic pancreatitis (9.5 E/ml, 4.9--26.5 E/ml), 7 patients with acute pancreatitis (14.2 E/ml, 5.5--67.3 ng/ml), and 13 patients with other types of malignomas (15 E/ml, 4.3--42.5 E/ml). Serum CEA level was evaluated in 18 "normal" patients (1.15 ng/ml, 0--4.3 ng/ml), 12 patients with pancreatic carcinoma (T3 or metastases) (6.5 mg/ml, 2--456.5 ng/ml), 13 patients with chronic pancreatitis (2.3 ng/ml, 0--8.5 ng/ml), 8 patients with acute pancreatitis (2.7 ng/ml, 0.1--4.6 ng/ml) and 5 patients without operative verification of suspected pancreatic carcinoma (0.9 ng/ml, 0--1.7 ng/ml). The serum RNase activity in pancreatic cancer patients did not show any significant increase in comparison to the other groups, and these patients could not be distinguished from those with the other diseases when excluding other factors influencing serum RNase level such as: Renal insufficiency, nutrition, age, sex. Their CEA level was significantly higher in comparison to the other groups (p less than 0.05). Using 2.5 ng/ml as the limit, the sensitivity was found to be 80% (10/12 of pancreatic carcinomas positive) and the specificity being 70.5% (31/44 of other groups without malignant diseases negative). The presented study and data in the literature show that poly (C) RNase measurement is not useful in early detection of pancreatic carcinoma, but the CEA test could be helpful in the differential diagnosis of pancreatic diseases due to its specificity (70.5%) and seems to be valuable in detection of residual and in monitoring for recurrent pancreatic carcinoma in view of its sensitivity and correlation with the stage of cancer.