Designing a broad-spectrum integrative approach for cancer prevention and treatment

Targeted therapies and the consequent adoption of "personalized" oncology have achieved notable successes in some cancers; however, significant problems remain with this approach. Many targeted therapies are highly toxic, costs are extremely high, and most patients experience relapse after a few disease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistant immortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are not reliant upon the same mechanisms as those which have been targeted). To address these limitations, an international task force of 180 scientists was assembled to explore the concept of a low-toxicity "broad-spectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspects of relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a wide range of high-priority targets (74 in total) that could be modified to improve patient outcomes. For these targets, corresponding low-toxicity therapeutic approaches were then suggested, many of which were phytochemicals. Proposed actions on each target and all of the approaches were further reviewed for known effects on other hallmark areas and the tumor microenvironment. Potential contrary or procarcinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixed evidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of the relationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. This novel approach has potential to be relatively inexpensive, it should help us address stages and types of cancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for future research is offered.

Therapeutic targeting of replicative immortality

One of the hallmarks of malignant cell populations is the ability to undergo continuous proliferation. This property allows clonal lineages to acquire sequential aberrations that can fuel increasingly autonomous growth, invasiveness, and therapeutic resistance. Innate cellular mechanisms have evolved to regulate replicative potential as a hedge against malignant progression. When activated in the absence of normal terminal differentiation cues, these mechanisms can result in a state of persistent cytostasis. This state, termed “senescence,” can be triggered by intrinsic cellular processes such as telomere dysfunction and oncogene expression, and by exogenous factors such as DNA damaging agents or oxidative environments. Despite differences in upstream signaling, senescence often involves convergent interdependent activation of tumor suppressors p53 and p16/pRB, but can be induced, albeit with reduced sensitivity, when these suppressors are compromised. Doses of conventional genotoxic drugs required to achieve cancer cell senescence are often much lower than doses required to achieve outright cell death. Additional therapies, such as those targeting cyclin dependent kinases or components of the PI3K signaling pathway, may induce senescence specifically in cancer cells by circumventing defects in tumor suppressor pathways or exploiting cancer cells’ heightened requirements for telomerase. Such treatments sufficient to induce cancer cell senescence could provide increased patient survival with fewer and less severe side effects than conventional cytotoxic regimens. This positive aspect is countered by important caveats regarding senescence reversibility, genomic instability, and paracrine effects that may increase heterogeneity and adaptive resistance of surviving cancer cells. Nevertheless, agents that effectively disrupt replicative immortality will likely be valuable components of new combinatorial approaches to cancer therapy.

Disruption of an hTERT-mTOR-RAPTOR protein complex by a phytochemical perillyl alcohol and rapamycin

We previously demonstrated in prostate cancer cells that a phytochemical-perillyl alcohol-and the mechanistic target of rapamycin (mTOR) inhibitor rapamycin rapidly attenuated telomerase activity. Protein levels of the telomerase catalytic subunit reverse transcriptase (hTERT) were diminished in the absence of an effect on hTERT mRNA, supporting an effect on 4E-BP1 phosphorylation and reduced initiation of protein translation. The decline in hTERT protein did not coincide wholly, however, with loss of telomerase activity suggesting a further level of regulation. We hypothesized that a hTERT-mTOR-S6K (S6 kinase)-Hsp90 (Heat shock protein 90)-Akt complex previously detected in activated NK cells was present in DU145 prostate cancer cells. Furthermore, we postulated that both perillyl alcohol and rapamycin disrupted this complex to control telomerase activity post-translationally. Antibodies directed against either RAPTOR, a binding partner of mTOR, or mTOR itself co-immunoprecipitated Hsp90, hTERT, and S6K confirming a similar TERT complex in prostate cancer cells. Perillyl alcohol or rapamycin caused rapid dissociation of the captured hTERT-mTOR-RAPTOR complex, establishing an additional mechanism by which these agents decrease telomerase activity. These findings provide convincing evidence for mTOR-mediated regulation of hTERT in DU145 cells.

Xeroderma pigmentosum variant: complementary molecular approaches to detect a 13 base pair deletion in the DNA polymerase eta gene

Deficiencies of DNA polymerase eta-an enzyme mediating replication past UV-induced DNA damage-predispose individuals to xeroderma pigmentosum variant (XPV) and result in a high incidence of skin cancers. We designed, developed and assessed several complementary molecular approaches to detect a genetically inherited deletion within DNA polymerase eta. RNA was reverse transcribed from XPV fibroblasts and from normal human cells, and standard polymerase chain reaction (PCR) was conducted on the cDNA targeting a region with a 13 base pair deletion within the polymerase eta gene. PCR products were subjected to restriction fragment length polymorphism (RFLP) analysis and cycle DNA sequencing. The deletion was found to eliminate a BsrGI restriction site and affected the number of resultant fragments visualized after gel electrophoresis. Cycle sequencing of polymerase eta-specific amplicons from XPV and normal cells provided a second approach for detecting the mutation. Additionally, the use of a fluorescent nucleic acid dye-EvaGreen-in real-time PCR and melt curve analysis distinguished normal and XPV patient-derived amplicons as well as heteroduplexes that represent heterozygotic carriers without the need for high resolution melt analysis-compatible software. Our approaches are easily adaptable by diagnostic laboratories that screen for or verify genetically inherited disorders and identify carriers of a defective gene.

Perillyl alcohol and genistein differentially regulate PKB/Akt and 4E-BP1 phosphorylation as well as eIF4E/eIF4G interactions in human tumor cells

Previously we demonstrated that secondary products of plant mevalonate metabolism called isoprenoids attenuate 3-hydroxy-3-methylglutaryl coenzyme A reductase mRNA translational efficiency and cause tumor cell death. Here we compared effects of "pure" isoprenoids (perillyl alcohol and gamma-tocotrienol) and a "mixed" isoprenoid-genistein-on the PKB/Akt/mTOR pathway that controls mRNA translation and m(7)GpppX eIF4F cap binding complex formation. Effects were cell- and isoprenoid-specific. Perillyl alcohol and genistein suppressed 4E-BP1(Ser65) phosphorylation in prostate tumor cell lines, DU145 and PC-3, and in Caco2 adenocarcinoma cells. Suppressive effects were similar to or greater than that observed with a PI3 kinase inhibitor or rapamycin, an mTOR inhibitor. 4E-BP1(Thr37) phosphorylation was reduced by perillyl alcohol and genistein in DU145, but not in PC-3. Conversely, perillyl alcohol but not genistein decreased 4E-BP1(Thr37) phosphorylation in Caco2. PKB/Akt activation via Ser473 phosphorylation was enhanced in DU145 by perillyl alcohol and in PC-3 by gamma-tocotrienol, but was suppressed by genistein. Importantly, perillyl alcohol disrupted interactions between eIF4E and eIF4G, key components of eIF4F (m(7)GpppX) cap binding complex. These results demonstrate that "pure" isoprenoids and genistein differentially impact cap-dependent translation in tumor cell lines.

Presence of the anti-leukemic nucleotide analog, 2-chloro-2'-deoxyadenosine-5'-monophosphate, in a promoter sequence alters DNA binding of TATA-binding protein (TBP)

2-Chlorodeoxyadenosine (CldAdo, Cladribine), a nucleoside analog used in the treatment of hairy cell leukemia, is phosphorylated and incorporated into DNA, but is not an absolute chain terminator. We hypothesized that the presence of a chlorine molecule projecting into the DNA minor groove would affect DNA:protein-binding interactions. Here, we investigated recognition of and binding to double-stranded CldAMP-substituted TATA promoter sequences by human TATA-binding protein (TBP) using mobility shift assays. Depending on the site, CldAMP in place of dAMP within a TATA sequence decreased in vitro TBP binding by approximately 30% to 55% compared to control sites. When bound to a CldAMP-substituted TATA box, however, the TBP complex was more resistant to polyanions, suggesting enhanced stability. Limited exposure of the TBP:DNA complex to proteases indicated that TBP conformation was altered on CldAMP-substituted DNA compared to control. Further, binding of transcription factor IIB to TBP was diminished on analog-containing TATA sequences. These results suggest normal TBP-binding interactions--specifically recognition, stability, and conformation-are disrupted by CldAMP insertion into eukaryotic promoter sequences.

The Antileukemia Drug 2-Chloro-2′-deoxyadenosine: An Intrinsic Transcriptional Antagonist

The nucleoside analog 2-chloro-2'-deoxyadenosine (CldAdo; cladribine) is effective in the treatment of hairy cell leukemia and chronic lymphocytic leukemia. CldAdo is phosphorylated and incorporated into cellular DNA but is not an absolute chain terminator. We demonstrated by in vitro gel-shift assays that binding interactions of the human TATA box-binding protein (TBP) were disrupted on 2-chlorodeoxyadenosine monophosphate (CldAMP)-substituted TATA box consensus sequences. We hypothesized that human RNA polymerase II (pol II) transcriptional processes would therefore be affected by 2-chlorodeoxyadenosine triphosphate (CldATP) incorporation into a promoter TATA element. Double-stranded DNA templates containing the adenovirus major late promoter and coding sequences were enzymatically synthesized as control or with site-specific CldAMP residues, incubated with HeLa extract, and the synthesis of radiolabeled 44-base transcripts was assessed. With increasing amounts of HeLa extract, CldAMP substitution for dAMP within the TATA box decreased in vitro pol II transcription by approximately 35% compared with control substrates. Time-course studies showed that transcript production increased in a linear fashion on control substrates. In contrast, transcription on CldAMP-substituted TATA sequences reached a plateau after 20 min. Furthermore, CldAMP-substituted promoter sequences trapped or sequestered TBP, preventing its dissociation from DNA and subsequent binding to additional TATA elements to reinitiate transcription. CldAdo thus represents the first example of a nucleoside analog that acts as a transcriptional antagonist. CldATP incorporation into gene regulatory sequences may provide a novel strategy to modulate specific protein/DNA interactions.

2-Chloro-2'-deoxyadenosine: alteration of DNA:TATA element binding protein (TBP) interactions

2-Chloro-2'-deoxyadenosine (CldAdo, cladribine) is used therapeutically for hairy cell and other leukemias. The nucleoside is converted in leukemia cells to the 2-Cl-analog of dATP and incorporated into DNA, where it may alter binding of transcription factors to gene regulatory AT-rich sequences. Here we model the effects of CldATP incorporation into the adenovirus major late promoter TATA element recognized by TATA binding protein (TBP). The modeling results are consistent with experimental studies of DNA:TBP binding and indicate which positions in the canonical TATA sequence are most severely affected by CldATP incorporation.FIGURE Structure of the DNA:TBP complex. The protein is shown as a ribbon structure, and the DNA as a stick model

Nucleotide excision repair-deficient human cells in culture exhibit decreased survival after 2-chlorodeoxyadenosine treatment

2-Chloro-2'-deoxyadenosine (CldAdo, cladribine) is a clinically important nucleoside analog for adult and pediatric leukemias. We previously described an activity in HeLa cell nuclear extracts that specifically recognized CldAMP-substituted oligomers. The factor was present in extracts prepared from repair-deficient xeroderma pigmentosum (XP) complementation group A cells, but not from group E--which are defective in damaged DNA-binding (DDB) protein--suggesting a possible repair process for incorporated analogs. Here we examined XP lymphoblast survival after CldAdo treatment using a cell proliferation assay. Control CEM leukemia cells and immortalized normal human lymphoblasts exhibited similar cytotoxicity profiles at each concentration tested. However, a 2.1-fold increase in sensitivity to CldAdo was detected in XP-E (5) cells lacking a functional DDB subunit. XP-A, XP-D and XP-G cell lines also had increased sensitivity to CldAdo, ranging from 1.61- to 1.91-fold greater compared to normal lymphoblasts. Our findings suggest that the clinical efficacy of CldAdo may be attenuated by repair mechanisms that target and remove such altered nucleic acids from cellular DNA.

Sterol-independent regulation of 3-hydroxy-3-methylglutaryl coenzyme A reductase in tumor cells

Elevated 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase expression supports synthesis of prenyl pyrophosphate intermediates required for tumor growth. In this study, the copy number of HMG-CoA reductase mRNA was determined in solid tumor and leukemic cell lines using competitive reverse transcriptase-polymerase chain reaction. Reductase mRNA was increased about eight-fold in Caco2 human colon adenocarcinoma cells compared with that in CCD18 normal colon cells. We also found a 50-fold enhancement of reductase mRNA in stimulated human lymphocytes compared with unstimulated cells. In CEM human leukemia cells, reductase mRNA was increased 8.6 times compared with that in stimulated lymphocytes. Greater low density lipoprotein receptor mRNA was also observed in tumor cells compared with normal counterparts. We hypothesized that elevated reductase mRNA was due to attenuation of sterol-mediated control of tumor reductase promoter activity. We first compared the methylation status of CpG dinucleotides in the promoters of reductase and p16 tumor suppressor genes from solid tumor, leukemic, and normal cells. As reported for other tumor cells the p16 promoter region was hypermethylated in Caco2 and CEM cells but was hypomethylated in corresponding normal cells. However, reductase promoter sequences in both normal and tumor cells were hypomethylated, demonstrating that methylation is not involved in sterol-independent reductase regulation. We addressed altered transcription factor binding to the tumor cell reductase promoter by transiently transfecting Caco2 and CCD18 with a plasmid vector containing a hamster HMG-CoA reductase promoter fused to the luciferase gene. We found that increased reductase mRNA was partially due to an approximately three-fold higher reductase promoter activity in Caco2 than in CCD18, measured by luciferase reporter assays. Thus, differential binding of transcription factor or factors on the tumor cell reductase promoter attenuates normal sterol-mediated regulation of reductase activity.

Isoprenoid-mediated inhibition of mevalonate synthesis: potential application to cancer

Pure and mixed isoprenoid end products of plant mevalonate metabolism trigger actions that suppress 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase activity. These actions modulate HMG CoA reductase mRNA translation and the proteolytic degradation of HMG CoA reductase. Such post-transcriptional events, we propose, are activated directly by acyclic isoprenoids and indirectly by cyclic isoprenoids. Isoprenoids, acting secondarily to the dominant transcriptional effector of sterologenesis, modestly lower cholesterol levels, if and only if, sterologenesis is not repressed by a saturating imput of dietary cholesterol. An anomaly associated with tumor growth-a sterol feedback-resistant HMG CoA reductase activity-ensures a pool of sterologenic pathway intermediates. Such intermediates provide lipophilic anchors essential for membrane attachment and biological activity of growth hormone receptors, nuclear lamins A and B, and oncogenic ras. Tumor HMG CoA reductase retains high sensitivity to the isoprenoid-mediated secondary regulation. Repression of mevalonate synthesis by plant-derived isoprenoids reduces ras and lamin B processing, arrests cells in G1, and initiates cellular apoptosis. This unique tumor cell-specific sensitivity allows isoprenoids to be used for tumor therapy, an application emulating that of the statins, but one free of adverse effects. When evaluated at levels provided by a typical diet, isoprenoids individually have no impact on cholesterol synthesis and tumor growth. Nonetheless, isoprenoid-mediated activities are additive, and, sometimes synergistic. Therefore, the combined actions of the estimated 23,000 isoprenoid constituents of plant materials, acting in concert with other chemopreventive phytochemicals, may explain the lowered cancer risk associated with a diet rich in plant products. In contrast, that lowering of cancer risk does not correspond to supplemental intake of other dietary factors associated with fruits, vegetables, and cereal grains, namely fiber, beta-carotene, vitamin C, and vitamin E, and only weakly to supplemental folate.

Isoprenoid-mediated inhibition of mevalonate synthesis: potential application to cancer

Pure and mixed isoprenoid end products of plant mevalonate metabolism trigger actions that suppress 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase activity. These actions modulate HMG CoA reductase mRNA translation and the proteolytic degradation of HMG CoA reductase. Such post-transcriptional events, we propose, are activated directly by acyclic isoprenoids and indirectly by cyclic isoprenoids. Isoprenoids, acting secondarily to the dominant transcriptional effector of sterologenesis, modestly lower cholesterol levels, if and only if, sterologenesis is not repressed by a saturating imput of dietary cholesterol. An anomaly associated with tumor growth-a sterol feedback-resistant HMG CoA reductase activity-ensures a pool of sterologenic pathway intermediates. Such intermediates provide lipophilic anchors essential for membrane attachment and biological activity of growth hormone receptors, nuclear lamins A and B, and oncogenic ras. Tumor HMG CoA reductase retains high sensitivity to the isoprenoid-mediated secondary regulation. Repression of mevalonate synthesis by plant-derived isoprenoids reduces ras and lamin B processing, arrests cells in G1, and initiates cellular apoptosis. This unique tumor cell-specific sensitivity allows isoprenoids to be used for tumor therapy, an application emulating that of the statins, but one free of adverse effects. When evaluated at levels provided by a typical diet, isoprenoids individually have no impact on cholesterol synthesis and tumor growth. Nonetheless, isoprenoid-mediated activities are additive, and, sometimes synergistic. Therefore, the combined actions of the estimated 23,000 isoprenoid constituents of plant materials, acting in concert with other chemopreventive phytochemicals, may explain the lowered cancer risk associated with a diet rich in plant products. In contrast, that lowering of cancer risk does not correspond to supplemental intake of other dietary factors associated with fruits, vegetables, and cereal grains, namely fiber, beta-carotene, vitamin C, and vitamin E, and only weakly to supplemental folate.

Analysis of 2-chloro-2'-deoxyadenosine incorporation into cellular DNA by quantitative polymerase chain reaction

Thermus aquaticus (Taq) DNA polymerase elongation is blocked by several DNA adducts. This property has been exploited in polymerase chain reaction (PCR) methods to analyze cellular DNA damage and repair after exposure to damaging agents. Such methods have not been applied previously to detect nucleoside analog incorporation into cellular DNA. 2-Chloro-2'-deoxyadenosine (CldAdo), a deoxyadenosine analog, is clinically effective for hairy cell leukemia. CldAdo is taken up by cells, converted to the triphosphate, and incorporated into cellular DNA. Here, we measured by primer extension the ability of CldAMP residues in 98-base single-stranded DNA to block Taq elongation. In contrast to control DNA, no full-length 98-mers were produced on CldAMP-containing templates, and Taq polymerase was halted at the first CldAMP site. We then examined the possibility of using quantitative PCR to measure CldATP incorporation into the N-ras gene after incubation of cultured human leukemia cells with CldAdo or with cisplatin as a positive control for DNA damage. Treatment with either drug resulted in reduced amounts of amplified DNA product compared to untreated cells. CldAMP residues within cellular DNA inhibited PCR amplification in a dose-dependent manner; 100 nM CldAdo produced approximately 0.4 CldAMP sites within a 523-bp region of the N-ras sequence. Thus, PCR analysis with Taq polymerase provides a sensitive assessment of nucleoside analog incorporation after cellular exposure to antileukemic drugs.

2-Chloro-2'-deoxyadenosine, an antileukemic drug, has an early effect on cellular mitochondrial function

2-Chloro-2'-deoxyadenosine [CldAdo (cladribine)], a novel effective antileukemic agent, was examined for its effects on cellular mitochondrial function and DNA content after long term (< or = 7-day) incubation of cultured CCRF-CEM human leukemia cells. Dideoxycytidine (ddC), which is known to have a delayed effect on mitochondrial DNA content, was used as a positive control to monitor mitochondrial dysfunction. CldAdo at 6-16 nM was toxic to cells within 24 hr, which is in contrast to 300 nM ddC, which had no effect on cell growth for the first 4 days of treatment. Cellular lactic acid production was used to monitor concomitant perturbations in oxidative phosphorylation during drug treatment. Unlike the delayed increase in lactate observed with ddC exposure, CldAdo-treated cells exhibited a 2-2.4-fold increase in lactate levels after 2 days of exposure to 16 nM CldAdo. By days 4 and 7, however, lactate production returned to control levels. Shorter incubations with CldAdo revealed that lactate levels began to increase within 12 hr of drug exposure, paralleling cytotoxicity. We also examined mitochondrial DNA content during drug treatment by competitive polymerase chain reaction. ddC (300 nM) reduced mitochondrial DNA levels from approximately 1000 copies/untreated cell to approximately 130 copies/cell after 7 days of exposure. In contrast, cytotoxic doses of CldAdo had little or no effect on mitochondrial DNA content during the 1-week incubation. Thus, the early CldAdo-induced perturbation of mitochondrial function was not associated with a loss of mitochondrial DNA per cell. In addition, no evidence of DNA laddering, indicative of cellular apoptosis, was detected at these dosage levels and treatment times.

In vitro transcription of DNA containing 2-chloro-2'-deoxyadenosine monophosphate

2-Chloro-2'-deoxyadenosine (cladribine [CldAdo]) represents one of the most promising therapeutic agents for the treatment of pediatric leukemias and adult hairy cell leukemia. We examined whether CldAdo incorporation into DNA inhibited subsequent transcription in vitro using purified phage RNA polymerases. Control (Ade-containing) and 2-chloroadenine (ClAde)-substituted DNA strands that contained a RNA polymerase promoter sequence were synthesized by a modified asymmetric polymerase chain reaction. Complementary (+) and (-) strands were annealed, incubated with phage RNA polymerase, and analyzed with denaturing PAGE. When ClAde was present in both strands, the yield of full-length transcripts (approximately equal to 100 bases) was reduced by approximately equal to 90% relative to control DNA. Transcription was also reduced to a slightly lesser degree when substitutions occurred in only one of two strands. The observed low transcript levels on ClAde-containing DNA were due in part to the presence of the analogue within the promoter region. With gel shift binding assays, we demonstrated that RNA polymerase did not bind as well to ClAde-containing promoters. Polymerase/DNA complex formation was decreased by approximately equal to 80% compared with that on control unsubstituted promoters. In addition, on binding to the substituted promoter, RNA polymerase had an altered conformation that led to enhanced proteolytic clipping by endoproteinase Glu-C. Transcript sequence analysis indicated that SP6 RNA polymerase read through template ClAde residues with no apparent misincorporation into RNA. Our results provide insight into a novel effect of this nucleoside analogue that may explain its cytotoxicity in nondividing cells.

A human factor that recognizes DNA substituted with 2-chloroadenine, an antileukemic purine analog

2-Chloro-2'-deoxyadenosine (cladribine), an analog of deoxyadenosine, is an important new drug for the treatment of hairy cell leukemia and other forms of adult and pediatric leukemia. By a gel-shift binding assay, we identified an activity in HeLa nuclear extracts that recognizes and binds to oligonucleotides substituted with 2-chloroadenine (ClAde). The activity was specific for ClAde residues because control oligomers did not readily compete out the complex. The binding factor was a monomeric protein that was resistant to inactivation by heating at 45 degrees C but sensitive to heating at 65 degrees C, proteinase K treatment, and 5 mM ZnCl2. This protein, designated ClAde recognition protein (CARP), appeared to be related to a protein that recognized other forms of DNA damage. Gel-shift binding reactions with ultraviolet (UV)-irradiated oligomers revealed a UV-specific protein/DNA complex that had an electrophoretic mobility similar to that of the CARP/DNA complex, and CARP binding to ClAde-containing oligomers was readily competed out by UV-irradiated DNA. Moreover, CARP activity was present in extracts prepared from UV-sensitive xeroderma pigmentosum group A cells but not in a subset of cells from group E, suggesting that CARP was similar to a previously described repair associated factor, xeroderma pigmentosum-E binding factor. Our findings support a possible repair process for ClAde residues incorporated into cellular DNA.

2-Chloro-2'-deoxyadenosine monophosphate residues in DNA enhance susceptibility to 3'-->5' exonucleases

2-Chloro-2'-deoxyadenosine triphosphate, a purine nucleotide analogue and potent antileukaemic agent, was incorporated into double-stranded 36-mers in place of dATP to investigate the effects of 2-chloroadenine (ClAde) on DNA polymerase-associated 3'-->5' exonuclease activity. ClAde residues within one strand of duplex DNA did not inhibit exonuclease activity; on the contrary, ClAde-containing minus strands were digested to a greater extent than was control DNA in the absence of deoxyribonucleoside triphosphates by Escherichia coli Klenow fragment, yeast DNA polymerase II and T4 DNA polymerase. After a 30 min incubation with 5 units of Klenow fragment, approximately 65% of control DNA remained in DNA fragments of 26 bases or larger compared with only approximately 25% of ClAde-substituted substrates. Unsubstituted plus strands opposite a ClAde-containing strand were likewise digested more quickly by 3'-->5' exonuclease, but only in the vicinity of the ClAde sites. Approx. 63% of the plus strands from ClAde-containing oligomers were less than 24 bases in length after a 25 min digestion period with Klenow fragment compared with only approximately 32% of control DNA. Such results indicate that, unlike other base modifications such as pyrimidine dimers, methoxy psoralen adducts and certain nucleoside analogues, all of which inhibit or decrease the rate of strand degradation by 3'-->5' exonucleases, incorporated ClAde enhances strand degradation of duplex DNA.

Template 2-chloro-2'-deoxyadenosine monophosphate inhibits in vitro DNA synthesis

2'-Chloro-2'-deoxyadenosine triphosphate (cladribine), a purine nucleotide analog and potent antileukemic agent, was enzymatically incorporated into 98-base oligomers in place of dATP to investigate the molecular consequences of 2-chloroadenine (CIAde) in DNA. We have used the resultant oligomers as templates for purified DNA polymerases, to compare the rate and extent of in vitro DNA synthesis; the sites of polymerase pausing, if any; and the effects of increasing deoxyribonucleoside triphosphate (dNTP) concentrations on synthetic reactions. Compared with control template, CIAde-containing DNA strikingly reduced the overall amount and rate of chain elongation by human polymerase beta and Klenow fragment. Distinct pause sites, which were polymerase dependent, occurred primarily one or two bases before or just after nucleotide incorporation opposite template CIAde. Human polymerase alpha and phage T4 DNA polymerase likewise exhibited reduced synthesis on CIAde-substituted templates. Bypassing of CIAde residues was possible only at higher dNTP concentrations, with approximately 20- and 50-fold greater dNTP concentrations being required for synthesis beyond CIAde sites, compared with adenine residues, by polymerase alpha and beta, respectively. These results suggest that CiAde residues located within cellular template DNA may inhibit daughter strand synthesis and thus contribute to the cytotoxic effects of the drug.

Establishment of hypoxic conditions for cultured monolayer cells: hypoxia in five minutes or less

A versatile deaeration chamber for altering the gaseous environment of monolayer cell cultures has been developed. The design is such that multiple samples of radioactively labeled or unlabeled cells can be gassed simultaneously with a short period of time. Deaeration times to reduce the level of oxygen in initially aerated cellular medium to very low levels (less than 20 parts per million) were decreased at least 6- to 20-fold when compared to most other methods commonly used to achieve N2- or N2O-induced hypoxia. The application of this chamber in the investigation of radiation-induced cellular DNA strand breaks, which are very sensitive to the presence of oxygen, is described. The vessel should be useful for a variety of metabolic and physiologic experiments or cell, tumor, and radiation biology studies.

Polymerase chain reaction amplification of single-stranded DNA containing a base analog, 2-chloradenine

By utilization of polymerase chain reaction techniques, single-stranded DNA of defined length and sequence containing a purine analog, 2-chloroadenine, in place of adenine was synthesized. This was accomplished by a combination of standard polymerase chain amplification reactions with Thermus aquaticus DNA polymerase in the presence of four normal deoxynucleoside triphosphates, M13 duplex DNA as template, and two primers to generate double-stranded DNA 118 bases in length. An asymmetric polymerase chain reaction, which produced an excess of single-stranded 98-base DNA, was then conducted with 2-chloro-2'-deoxy-adenosine 5'-triphosphate in place of dATP and with only one primer that annealed internal to the original two primers. Standard polymerase chain reaction techniques alone conducted in the presence of the analog as the fourth nucleotide did not produce duplex DNA that was modified within both strands. This asymmetric technique allows the incorporation of an altered nucleotide at specific sites into large quantities of single-stranded DNA without using chemical phosphoramidite synthesis procedures and circumvents the apparent inability of DNA polymerase to synthesize fully substituted double-stranded DNA during standard amplification reactions. The described method will permit the study of the effects of modified bases in template DNA on a variety of protein-DNA interactions and enzymes.

Effects of 2-chloroadenine substitution in DNA on restriction endonuclease cleavage reactions

The purine analog, 2-chloro-2'-deoxyadenosine triphosphate (CldATP), was incorporated enzymatically in place of dATP into the minus strand of M13mp18 duplex DNA. Its effect on protein-DNA interactions was assessed by determining the amount of DNA cleavage by type II restriction endonucleases. Substitution of chloroadenine (CIAde) for adenine (Ade) in DNA appreciably decreased the amount and rate of DNA cleavage of the minus strand when the analog was situated within the appropriate endonuclease recognition site. CIAde residues flanking a restriction site had variable effects. SmaI cleaved both CIAde-containing and control substrates with equal efficiency. NarI, however, was stimulated 1.5-fold by the presence of CIAde outside its recognition site. The effects of analog incorporation on restriction enzyme cleavage of an opposing unsubstituted strand of duplex DNA was examined by enzymatically incorporating CIdATP into the complementary minus strand of a 36-base oligonucleotide. Endonucleolytic cleavage of both plus and minus strands was reduced on 36-mers containing CIAde residues located within only the minus strand. These data suggest that CIAde residues incorporated into a single DNA strand may have an appreciable effect on DNA-protein interactions that involve one or both strands of duplex DNA.

Effects of 2-chloro-2'-deoxyadenosine 5'-triphosphate on DNA synthesis in vitro by purified bacterial and viral DNA polymerases

2-Chloro-2'-deoxyadenosine 5'-triphosphate (CldATP) was compared with dATP as a substrate for DNA synthesis by bacterial and viral DNA polymerases in vitro. Lengths of chain extension and DNA synthesis pause sites were determined by comparison with products generated by dideoxynucleotide sequencing methods on the same end-labeled primer/template duplex after high-resolution polyacrylamide gel electrophoresis. Reverse transcriptase (RT) from human immunodeficiency virus (HIV-1) and avian myeloblastosis virus (AMV) incorporated CldATP efficiently. DNA strand elongation continued past most chloroadenine (ClA) insertion sites but resulted in shorter chains than when dATP was inserted. Phage T4 DNA polymerase incorporated CldATP least efficiently; Klenow fragment of Escherichia coli DNA polymerase I and modified T7 DNA polymerase (Sequenase) showed intermediate ability to utilize the analogue. Incorporation of several consecutive ClA residues into the replicating strand dramatically reduced the ability of Sequenase, Klenow fragment, and T4 DNA polymerases to continue strand elongation. In the absence of the corresponding normal deoxyribonucleoside triphosphate during DNA synthesis, ClA was frequently misincorporated as thymine, cytosine, or guanine by both AMV RT and HIV-1 RT but rarely, if at all, by Klenow fragment, Sequenase, and T4 DNA polymerase. Except T4, for most DNA polymerases, CldATP at 10-20-fold molar excess over dATP was not a strong competitive inhibitor of dATP, as judged by the amount of strand extension and polymerase pause sites during DNA synthetic reactions. Our results indicate that the degree of strand extension in the presence of CldATP, the number and location of polymerase pause sites, and the amount of misincorporation of the analogue are both polymerase- and sequence-dependent.

Genetic and biochemical characterization of the CHO-UV-1 mutant defective in postreplication recovery of DNA

The CHO-UV-1 mutant, a Chinese hamster ovary cell with defective postreplication recovery of DNA, is 2- to 4-fold more sensitive than its wild-type counterpart (CHO-77256) to the lethal effects of ethylating agents and UV radiation; it is also hypersensitive (10- to 20-fold) to some DNA-methylating and -cross-linking agents. We studied the CHO-UV-1 mutant further to define its phenotype in terms of DNA damage induction and repair, methyltransferase activity, and effects of caffeine on mutational and lethal responses. Both wild-type and CHO-UV-1 cells incurred similar levels and types of damage when exposed to UV radiation, N-methyl-N'-nitro-N-nitrosoguanidine, or N-methyl-N-nitrosourea. The rate and extent of repair of Micrococcus luteus endonuclease-sensitive sites after UV irradiation or treatment with N-methyl-N'-nitro-N-nitrosoguanidine were also equivalent in these two cell types. Twenty % of the initial endonuclease-sensitive sites induced in either cell line remained at 18 h after UV irradiation; approximately 8% of the sites after N-methyl-N'-nitro-N-nitrosoguanidine exposure were present in both parental and CHO-UV-1 cells after a 17-h repair period. Moreover, the ability of CHO-UV-1 to resynthesize and ligate DNA during excision repair was similar to that of its parent. Neither CHO-UV-1 nor CHO-77256 had appreciable levels of O6-methylguanine-DNA methyltransferase activity which ameliorates the cytotoxicity of alkylating agents. Caffeine, a known inhibitor of postreplication repair, decreased the frequency of mutation induction at the hypoxanthine-guanine phosphoribosyltransferase locus by 40-55% in CHO-77256 but not in CHO-UV-1. These results rule out defective excision repair as a factor in the hypersensitivity of the CHO-UV-1 mutant to DNA-damaging agents. Hence, this cell line appears to derive from a mutation affecting nonexcision repair processes and should be useful in clarifying the mechanism(s) of postreplication recovery of DNA in mammalian cells.

Incorporation of 2-halogeno-2'-deoxyadenosine 5-triphosphates into DNA during replication by human polymerases alpha and beta

Extension of synthetic primers by purified human polymerase alpha (Hpol alpha) with the (+)-strand of M13mp18 DNA as template encounters numerous specific pause sites on the M13 template. Some of these are regions of template secondary structure, at others the template codes for incorporation of the same base in multiple consecutive positions, but at some the responsible feature in the sequence is not obvious. 2-Chloro-dATP (CldATP) substitutes efficiently for dATP in such chain extension, with 2-chloroadenine (ClA) incorporation into many positions coding for A. However, there are more sites where extension is interrupted than with all four normal nucleotide substrates, particularly (but not exclusively) at template secondary structure and sites of multiple consecutive ClA insertion. DNA synthesis from normal substrates by Hpol beta in this system shows less frequent and less marked pauses, but with CldATP substituted for dATP chain extension is limited because of marked slowing of extension at sites of multiple consecutive ClA insertion. With either polymerase, the rate of extension is decreased even more at such regions when bromo-dATP is used as substrate. Some misincorporation of ClA instead of G or T can occur at certain sites in absence of the corresponding normal substrate, but misincorporation as C is rare. CldATP is a very weak inhibitor of chain extension by Hpol alpha, but a somewhat better inhibitor of Hpol beta. These results may account in part for the inhibition of DNA synthesis in cells exposed to 2-chlorodeoxyadenosine or 2-bromodeoxyadenosine.

Induction and repair of DNA damage in gamma-irradiated human lymphoblasts: irradiation in the presence and absence of misonidazole

The effects of oxygen and misonidazole on the induction of DNA lesions were examined in human TK6 lymphoblasts irradiated with 60Co gamma rays. We have investigated both the formation and subsequent repair of two classes of DNA damage, single-strand breaks and lesions recognized by the gamma endonuclease activity in a cell-free extract of Micrococcus luteus. Relative to irradiation under hypoxia, single-strand break yields were increased by the presence of either oxygen or misonidazole at the time of irradiation. In contrast, M. luteus enzyme-sensitive site yields were unaffected by the presence of either oxygen or misonidazole. No significant differences in single-strand break or enzyme-sensitive site repair kinetics were observed for lesions induced under any of the irradiation conditions employed. These results confirm the sensitizing effects of oxygen and oxygen-mimetic drugs on the induction of single-strand breaks but provide no support for their ability to enhance the induction of enzyme-sensitive sites.

Sequence specificity of DNA cleavage by Micrococcus luteus gamma endonuclease

DNA fragments of defined sequence have been used to determine the sites of cleavage by gamma-endonuclease activity in extracts prepared from Micrococcus luteus. End-labeled DNA restriction fragments of pBR322 DNA that had been irradiated under nitrogen in the presence of potassium iodide or t-butanol were treated with M. luteus gamma endonuclease and analyzed on high resolution, denaturing, polyacrylamide gels. Gamma endonuclease was found to cleave irradiated DNA preferentially at the positions of cytosines and thymines. DNA cleavage occurred immediately to the 3' side of pyrimidines in irradiated DNA and resulted in fragments that terminate in a 5'-phosphoryl group. These studies indicate that both altered cytosines and thymines may be important DNA lesions requiring repair after exposure to gamma radiation.