Hindering auxiliary anchors are potent modulators of peptide binding and selection by I-Ak class II molecules.

Selection of particular antigen-derived peptides by class II MHC molecules determines the population of complexes represented on the antigen-presenting cell surface and available for T cell receptor engagement. This discriminating selection process results from unique interactions between the spectrum of peptides generated during antigen processing and the MHC molecules. Here, we examined the selection of peptides by the class II MHC, I-A(k). Our results indicate that although peptide primary anchors are key in MHC binding, auxiliary anchors are a powerful regulatory component in the selection of peptides by I-A(k). Study of the segments surrounding the dominant hen egg white lysozome(48-61) epitope demonstrates that auxiliary anchors also are involved in determining the binding register of I-A(k) along an extended peptide. In addition, we found that unique combinations of auxiliary anchors can act in concert to modulate the binding of peptides to I-A(k).

Structural basis of peptide binding and presentation by the type I diabetes-associated MHC class II molecule of NOD mice.

We have determined the crystal structure of I-Ag7, an integral component in murine type I diabetes development. Several features distinguish I-Ag7 from other non-autoimmune-associated MHC class II molecules, including novel peptide and heterodimer pairing interactions. The binding groove of I-Ag7 is unusual at both terminal ends, with a potentially solvent-exposed channel at the base of the P1 pocket and a widened entrance to the P9 pocket. Peptide binding studies with variants of the hen egg lysozyme I-Ag7 epitope HEL(11-25) support a comprehensive structure-based I-Ag7 binding motif. Residues critical for T cell recognition were investigated with a panel of HEL(11-25)-restricted clones, which uncovered P1 anchor-dependent structural variations. These results establish a framework for future experiments directed at understanding the role of I-Ag7 in autoimmunity.

Characterization and quantitation of peptide-MHC complexes produced from hen egg lysozyme using a monoclonal antibody.

Here we describe generation of Aw3.18, a monoclonal antibody that recognizes peptide residues 48-62 of hen egg lysozyme (HEL) bound to the MHC class II molecule I-Ak. Epitope mapping revealed that Aw3.18 detects a change in the solvent-exposed surface of this peptide-MHC complex upon substitution of the peptide side chain at position P1. Furthermore, Aw3.18 blocked recognition by some, but not all, of the HEL 48-62-reactive T cell hybridomas tested, suggesting a heterogeneity in the T cell response toward this complex. Finally, using Aw3.18, it was possible to determine the fraction of I-Ak molecules loaded with 48-62 peptide after culture of an antigen-presenting cell in medium containing HEL.

A negatively charged anchor residue promotes high affinity binding to the MHC class II molecule I-Ak.

An allele-specific peptide-binding motif for the murine MHC class II molecule I-Ak has proven elusive. Here we demonstrate that the I-Ak molecule preferentially binds peptides that contain negatively charged amino acids at the primary anchor position (Asp or Glu at P1), and that I-Ak can also bind peptides with polar residues at P1 (Cys, Ser, Asn, Gin, or Thr), although with lower affinity. This preference for a negatively charged anchor residue is so pronounced that polyalanine peptides containing a single Asp can bind to I-Ak. Eight naturally processed peptides were found to use an Asp, as demonstrated by a drop in the I-Ak binding affinity of these peptides after Ala substitution. The chemical identity of the amino acid in the anchor position was also important in determining the ability of peptide-I-Ak complexes to resist denaturation on SDS-polyacrylamide gels. The P1 binding pockets of HLA-DR and H-2E molecules are reported to be large and hydrophobic, and these class II molecules prefer to bind peptides with large aliphatic or aromatic side chains at P1. Our results suggest that the structure of the I-Ak P1 binding pocket is different. Based on sequence comparisons, we suggest that the P1 binding pockets of H-2A molecules may prove more polymorphic than the P1 binding pockets of H-2E molecules, and that this additional polymorphism will cause H-2A molecules to display larger intra-allelic differences in peptide binding specificities.

Peptides determine the lifespan of MHC class II molecules in the antigen-presenting cell.

Although many peptides are generated during the intracellular processing of protein antigens, only a few are selected for recognition by the immune system. The immunodominant epitope of hen egg white lysozyme (HEL) for H-2k mice is contained in a tryptic fragment of amino-acid residues 46-61 (refs 6, 7). The core of this T-cell epitope, from amino acids 52 to 61 (DYGILQINSR), contains those residues required for binding to the class II molecule I-Ak (ref. 7). Most of the naturally processed fragments recovered from I-Ak-bearing antigen-presenting cells (APCs) cultured with HEL contained this 52-61 core sequence, presented as a nested set of peptides with extensions at both the amino and carboxyl termini. We now compare the handling by APCs of peptides containing HEL 52-61 to establish whether there is an advantage for the APC in selecting extended peptides: different complexes between peptides and major histocompatibility complex (MHC) molecules varied greatly in the amount of time associated with the APC, and in their immunogenic strength. This difference in persistence is one of the factors contributing to the selection and immune recognition of peptide-MHC complexes by T cells.

Identification of two distinct properties of class II major histocompatibility complex-associated peptides.

We have examined the interactions of various peptides with the mouse class II major histocompatibility complex molecule I-Ak. The peptides were derived from the model protein hen egg white lysozyme (HEL). The immunodominant peptide of HEL is a 10-mer, residues 52-61. Our previous work established that this sequence contains the key residues for binding and presentation to T cells. Now we show that the binding of this 10-mer sequence resulted in complexes of I-Ak and peptide that, in SDS/PAGE (without boiling the protein), rapidly dissociated from the component alpha and beta chains. The binding interactions were studied in vitro, by incubating purified I-Ak and radiolabeled peptide, or ex vivo, by using antigen-presenting cells incubated with peptides. Peptides with additional residues at either the amino or carboxyl terminus behaved dramatically differently. Complexes of I-Ak with the longer peptides were stable to SDS/PAGE. Very few amino acid additions result in the change from unstable to stable complexes. The important issue here is that when cultured with HEL, antigen-presenting cells selected the HEL peptides containing the 52-61 sequences that favored stability [Nelson, C. A., Roof, R. W., McCourt, D. W. & Unanue, E. R. (1992) Proc. Natl., Acad. Sci. USA 89, 7380-7383]. Also, from other studies, such sequences correlate with a high immunogenicity of the peptide. We conclude that there are structural features of peptides that change the stability of the class II molecule and that are independent of the "core" peptide seen by the T cells.

Modulation of nitrosourea resistance in human colon cancer by O6-methylguanine.

Human colon cancer is resistant to a variety of alkylating agents including the nitrosoureas. To specifically evaluate nitrosourea resistance, we studied the role of O6-alkylguanine-DNA alkyltransferase (alkyltransferase) which is known to repair nitrosourea-induced cytotoxic DNA damage. Alkyltransferase activity varied over a similar wide range in 25 colon cancer biopsies and 14 colon cancer cell lines but the activity was not correlated with differentiation status, Dukes' classification or in vitro growth characteristics. 1,3-Bis-(2-chloroethyl)-1-nitrosourea (BCNU) resistance and alkyltransferase activity were highly correlated (R2 = 0.929, P less than 0.001) in 7 different colon cancer cell lines, suggesting that the alkyltransferase is an important component of nitrosourea resistance in colon cancer cells. In the BCNU-resistant, high alkyltransferase VACO 6 cell line, inactivation of the alkyltransferase by O6-methylguanine caused a proportional decrease in the BCNU IC50, consistent with that predicted by the regression line. Enzyme inactivation was also associated with a marked increase in DNA cross-link formation. Because alkyltransferase correlates with BCNU resistance in colon cancer, and resistance can be reversed by inactivating the protein, the alkyltransferase may have an important role in nitrosourea resistance in human colon cancer cells. These data provide the rationale for clinical trials in colon cancer with biochemical modulators of the alkyltransferase to increase the therapeutic response to nitrosoureas.

Mechanism of epipodophyllotoxin-induced cell death in poly(adenosine diphosphate-ribose) synthesis-deficient V79 Chinese hamster cell lines.

Mutant Chinese hamster V79 cells selected for alterations in poly(ADP-ribose) metabolism were shown to be resistant to epipodophyllotoxin (VP-16)-induced cytotoxicity. Cell lines ADPRT 54 and ADPRT 351 have reduced activity of poly(ADP-ribose) polymerase. N2, N3, and N4 cell lines grow in the absence of nicotinamide, with total NAD levels 1.5-3% of those found in parental V79 cells grown in complete medium. When grown in complete medium, the mutant cell lines are 2.3- to 9.6-fold resistant to VP-16-induced cytotoxicity. All of the cell lines respond to VP-16 treatment by formation of protein-cross-linked DNA strand breaks. Upon drug removal, all the cell lines reverse the DNA strand breaks at similar rates. Our studies show a clear dissociation between induction of DNA strand breaks and cytotoxicity. However, there is a good correlation between drug-induced sister chromatid exchanges and cytotoxicity. Thus, N3 cells, with low levels of VP-16-induced sister chromatid exchanges, show reduced levels of cytotoxicity relative to parental V79 cells, despite the fact that both cell lines show similar levels of VP-16-induced protein-cross-linked DNA strand breaks. Additional studies show that the time course of VP-16-induced cytotoxicity correlated better with the time course of sister chromatid exchange formation than with protein-cross-linked DNA strand break formation. These studies provide strong support for the proposal that VP-16-induced cytotoxicity involves the induction of sister chromatid exchanges. Thus, we suggest that drug-induced stabilization of topoisomerase II-DNA complexes stimulates induction of sister chromatid exchanges, which consequently lead to cell death.

Mutant cells defective in poly(ADP-ribose) synthesis due to stable alterations in enzyme activity or substrate availability.

We used two different approaches to develop cell lines deficient in poly(ADP-ribose) synthesis to help determine the role of this reaction in cellular functions. One approach to this problem was to develop cell lines deficient in enzyme activity; the other approach was to develop cell lines capable of growing with such low nicotinamide adenine dinucleotide (NAD) levels so as to effectively limit substrate availability for poly(ADP-ribose) synthesis. The selection strategy for obtaining cells deficient in activity of poly(ADP-ribose) polymerase was based on the ability of this enzyme to deplete cellular NAD in response to high levels of DNA damage. Using this approach, we first obtained cell lines having 37-82% enzyme activity compared to their parental cells. We now report the development and characterization of two cell lines which were obtained from cells having 37% enzyme activity by two additional rounds of further mutagenization and selection procedures. These new cell lines contain 5-11% enzyme activity compared to the parental V79 cells. In pursuit of the second strategy, to obtain cells which limit poly(ADP-ribose) synthesis by substrate restriction, we have now isolated spontaneous mutants from V79 cells which can grow stably in the absence of free nicotinamide or any of its analogs. These cell lines maintain NAD levels in the range of 1.5-3% of that found in their parental V79 cells grown in complete medium. The pathway of NAD biosynthesis in these NAD-deficient cells is not yet known. Further characterization of these lines showed that under conditions that restricted poly(ADP-ribose) synthesis, they all had prolonged doubling times and increased frequencies of sister chromatid exchanges.

Topoisomerase II-dependent and -independent mechanisms of etoposide resistance in Chinese hamster cell lines.

Resistance to etoposide (VP-16), amsacrine (mAMSA), and doxorubicin (Adriamycin) was studied in two Chinese hamster cell lines primarily selected for resistance to the epipodophyllotoxin. Both lines demonstrated profound resistance to VP-16, and mAMSA stimulated DNA breakage. However, the resistance to mAMSA cytotoxicity in both lines was less than expected from the level of resistance to the effects of topoisomerase II inhibition. Similarly, resistance to the cytotoxicity of high VP-16 concentrations in one of the lines was less than expected from the resistance to inhibition of topoisomerase II. An analysis of the relation of DNA breaks to drug cytotoxicity suggests that cross-resistance to mAMSA was mainly conferred through loss of mAMSA-stimulated, topoisomerase II-mediated DNA breaks. This mechanism also contributed towards reduced VP-16 cytotoxicity. However, our studies suggest that additional mechanisms, independent of resistance to VP-16-mediated topoisomerase II effects, greatly increased the resistance to this agent. Resistance to VP-16 cytotoxicity, not dependent on resistance to drug-mediated DNA cleavage, could be overcome at high drug concentrations in one of the resistant lines and might be responsible for the greater relative resistance to VP-16 than to mAMSA. These findings suggest the presence of two distinct mechanisms of resistance to VP-16 cytotoxicity, one presumably mediated by topoisomerase II and dependent on resistance to drug-mediated DNA scission, and a second mechanism independent of the effects of the drug on topoisomerase II.

Camptothecin hypersensitivity in poly(adenosine diphosphate-ribose) polymerase-deficient cell lines.

Mutant cell lines, derived from the Chinese hamster V79 cell line, deficient in poly(adenosine diphosphate-ribose) polymerase activity, and previously shown to be resistant to topoisomerase II inhibitors, were found to be hypersensitive to camptothecin, a topoisomerase I inhibitor. In all the cell lines, camptothecin induced dose-dependent protein-associated DNA single-strand breaks and sister chromatid exchanges. The increased sensitivity to camptothecin-induced cytotoxicity was not associated with an increase in DNA single strand breaks or sister chromatid exchanges. These results suggest the absence of any direct causal relation between (1) camptothecin induced sister chromatid exchanges and cytotoxicity or (2) camptothecin induced DNA strand breaks and cytotoxicity. The hypersensitivity of these mutant cell lines to camptothecin suggests that poly(adenosine diphosphate-ribose) polymerase is involved with topoisomerase I in modulating camptothecin induced cytotoxicity.

Strategy for selection of cell variants deficient in poly(ADP-ribose) polymerase.

A selection strategy to obtain cells deficient in poly(ADP-ribose) polymerase was developed based on the fact that treatment with high levels of N-methyl-N'-nitro-N-nitrosoguanidine results in sufficient activation of poly(ADP-ribose) polymerase to cause NAD and ATP depletion leading to cessation of all energy-dependent processes and rapid cell death. In contrast, cells with low levels of poly(ADP-ribose) polymerase should not consume their NAD and might therefore be more likely to survive the DNA damage. Using this approach, we have cloned a number of cell lines containing 37-82% enzyme activity. The apparent decrease in poly(ADP-ribose) polymerase activity is not due to increases in NAD glycohydrolase, poly(ADP-ribose) glycohydrolase, or phosphodiesterase activities. Further characterization of the poly(ADP-ribose) polymerase-deficient cells indicates that they have prolonged generation times and increased rates of spontaneous sister chromatid exchanges.

Poly(ADP-ribose) polymerase activity in proliferating and quiescent murine mammary carcinoma cells.

Previous studies have shown that the well-oxygenated but nutrient-deprived quiescent (QI) cells of the 67 murine mammary carcinoma line are significantly more sensitive to radiation-induced cell killing than the well-oxygenated proliferating (P) cells. These QI cells also sustain more initial strand breaks per radiation dose and repair them more slowly than do P cells. We now report that NAD+ levels and rates of poly(ADP-ribosylation) show a trend similar in that both these metabolic parameters are lower in QI cells by a factor of two or more. NAD+ levels were measured in acid extracts of intact monolayers using an enzymatic cycling assay, while poly(ADP-ribosylation) was followed through the incorporation of radioactive NAD+ into polymer by permeabilized cells. The major proteins labeled by [32P]NAD+ were the same in P and QI cells. However, qualitative differences exist among minor poly(ADP-ribosylated) proteins, with some bands labeled in P cells but not detectably labeled in QI cells. These studies suggest similarities between the physiological state of QI cells and that of mature resting lymphocytes.

Identification of minimal size requirements of DNA for activation of poly(ADP-ribose) polymerase.

Poly(ADP-ribose) polymerase requires DNA as an essential enzyme activator. Using enzyme purified from lamb thymus and double-stranded deoxynucleotide oligomers of defined length, we conducted studies to identify the smallest size DNA fragment capable of successfully activating poly(ADP-ribose) polymerase. These studies revealed that a double-stranded hexadeoxynucleotide activated the enzyme 30% as effectively as highly polymerized calf thymus DNA and a double-stranded octadeoxynucleotide activated the enzyme even more effectively than calf thymus DNA. When histone H1 was also included in the reaction system, the enzyme could be activated by even smaller DNA fragments. Thus, in the presence of histone H1, a double-stranded tetradeoxynucleotide activated the enzyme 25% as effectively as calf thymus DNA, and a double-stranded hexadeoxynucleotide was equally as effective as calf thymus DNA. The time courses for activation and the stabilities of the products were identical when the enzyme was activated by a double-stranded hexadeoxynucleotide or by calf thymus DNA. Double-stranded oligodeoxynucleotides containing dephosphorylated termini were more effective activators than those containing 3'-phosphorylated termini which in turn were more effective than those containing 5'-phosphorylated termini.

Modulation of nicotinamide adenine dinucleotide and poly(adenosine diphosphoribose) metabolism by the synthetic "C" nucleoside analogs, tiazofurin and selenazofurin. A new strategy for cancer chemotherapy.

Tiazofurin (2-beta-D-ribofuranosylthiazole-4-carboxamide) and selenazofurin (2-beta-D-ribofuranosylselenazole-4-carboxamide) are synthetic "C" nucleosides whose antineoplastic activity depends on their conversion to tiazofurin-adenine dinucleotide and selenazofurin-adenine dinucleotide which are analogs of NAD. The present study was conducted to determine whether these nucleoside analogs and their dinucleotide derivatives interfere with NAD metabolism and in particular with the NAD-dependent enzyme, poly(ADP-ribose) polymerase. Incubation of L1210 cells with 10 microM tiazofurin or selenazofurin resulted in inhibition of cell growth, reduction of cellular NAD content, and interference with NAD synthesis. Using [14C]nicotinamide to study the uptake of nicotinamide and its conversion to NAD, we showed that the analogs interfere with NAD synthesis, apparently by blocking formation of nicotinamide mononucleotide. The analogs also serve as weak inhibitors of poly(ADP-ribose) polymerase, which is an NAD-utilizing, chromatin-bound enzyme, whose function is required for normal DNA repair processes. Continuous incubation of L1210 cells in tiazofurin or selenazofurin resulted in progressive and synergistic potentiation of the cytotoxic effects of DNA-damaging agents, such as 1,3-bis(2-chloroethyl)-1-nitrosourea or N-methyl-N'-nitro-N-nitrosoguanidine. These studies provide a basis for designing chemotherapy combinations in which tiazofurin or selenazofurin are used to modulate NAD and poly(ADP-ribose) metabolism to synergistically potentiate the effects of DNA strand-disrupting agents.

Activation of poly(adenosine diphosphate ribose) polymerase by SV 40 minichromosomes: effects of deoxyribonucleic acid damage and histone H1.

Poly(ADP-ribose) polymerase is a chromosomal enzyme that is completely dependent on added DNA for activity. The ability of DNA molecules to activate the polymerase appears to be enhanced by the presence of DNA damage. In the present study, we used SV 40 DNA and SV 40 minichromosomes to determine whether different types of DNA damage and different chromosomal components affect stimulation of polymerase activity. Treatment of SV 40 minichromosomes with agents or conditions that induced single-strand breaks increased their ability to stimulate poly(ADP-ribose) synthesis. This stimulation was enhanced by addition of histone H1 at a ratio of 1 microgram of histone H1 to 1 microgram of DNA. Higher ratios of histone H1 to DNA suppressed the ability of SV 40 minichromosomes containing single-strand breaks to stimulate enzyme activity. Treatment of SV 40 minichromosomes or SV 40 DNA with HaeIII restriction endonuclease to produce double-strand breaks markedly stimulated poly(ADP-ribose) polymerase activity. The stimulation of poly(ADP-ribose) polymerase by double-strand breaks occurred in the absence of histone H1 and was further enhanced by adding histone H1 up to ratios of 2 to 1 relative to DNA. At higher ratios of histone H1 to DNA, the presence of the histone continued to enhance the poly(ADP-ribose) synthesis stimulated by double-strand breaks.

Purification and properties of poly(ADP-ribose) polymerase from lamb thymus.

Poly(ADP-ribose) polymerase was purified 2900-fold from lamb thymus with a recovery of 5%. Addition of exogenous DNA was essential for activity of the purified enzyme, and the reaction was stimulated by the addition of either a mixture of histones or purified histone H1. The enzyme is inhibited by sulfhydryl binding agents such as phenylmethanesulfonyl fluoride or N-ethylmaleimide. It does not require magnesium or other metal ion cofactors for activity. The enzyme migrated as a single polypeptide chain with an apparent molecular weight of 135 000 when gel electrophoresis was performed in the presence of sodium dodecyl sulfate. The apparent molecular weight was 175 000 when determined by gel filtration on Sepharose CL-6B-200. The isoelectric point was pH 9.6, and the pH optimum for activity was 8.6-8.8. The apparent Km for NAD+ was 160 microM at 37 degrees C. The activity of the purified polymerase was unaffected by the presence of ADP-ribose, 3',5'-cAMP, or NaF. Nicotinamide, 5-methyl-nicotinamide, theophylline, and thymidine markedly inhibited enzyme activity. Lamb thymus DNA, originally associated with the enzyme, was more effective than commercially obtained calf thymus DNA as an enzyme activator.

Association of poly(ADP-rib) synthesis with cessation of DNA synthesis and DNA fragmentation.

CHO cells and cs-4-D3 cells were used to investigate the association between poly(ADP-rib) synthesis and the cessation of DNA synthesis and DNA fragmentation. The cs4-D3 cells are cold-sensitive DNA synthesis arrest mutants of CHO cells. Upon incubation at 33 degrees C, DNA synthesis in the cs4-D3 cells stops and the cells enter a prolonged G1 or G0 phase. The events that occurred when cs4 cells were incubated at 33 degrees C were similar to those that occurred when wild-type CHO cells grew to high density. (1) In both cases, DNA synthesis and cell growth stopped. (2) The NAD+ concentration/cell was 20-25% lower in growth-arrested cells than in logarithmically growing cells. (3) Poly(ADP-rib) synthesis was 3-4 fold higher in growth-arrested cells than in logarithmically growing cells. (4) The growth-inhibited cells developed DNA strand breaks which resulted in large percentages of their DNA appearing in the low molecular weight range of alkaline sucrose gradients. (5) Both the increased rate of poly(ADP-rib) synthesis and the development of DNA strand breaks appears to be characteristic of the G1 phase of the cell cycle. (6) When growth-inhibited cells were restored to conditions favorable for DNA synthesis and cell growth, the DNA strand breaks were repaired. (7) Prolonged incubation under growth-restrictive conditions resulted in the accumulation of more DNA strand breaks than the cells could repair. This was followed by cell death when the cells were restored to conditions favorable for cell growth.