Abstract P3-07-09: Quantitative p95HER2 protein expression is predictive of trastuzumab response in HER2-positive metastatic breast cancer

Background: Expression of p95HER2 (p95), a truncated form of the HER2 receptor that lacks the trastuzumab binding site but retains kinase activity, has been reported as a prognostic biomarker for poor outcome in trastuzumab-treated HER2-positive metastatic breast cancer (MBC). However, the ability of p95 to predict trastuzumab benefit has not been demonstrated due to the difficulty in obtaining the appropriate control group, namely HER2+ MBC patients not treated with trastuzumab. In the current study, the predictive value of p95 expression was tested in a cohort comprised of HER2-positive MBC patients treated before the availability of trastuzumab and trastuzumab-treated HER2-positive MBC patients.

Methods: The current cohort was derived from 206 HER2-positive MBC patients in the Munich Cancer Registry with a median follow up of 64 months. Cases were divided between those that received trastuzumab (n=115) and those that were treated before the availability of trastuzumab (n=91). Quantitative p95 protein expression was measured in formalin-fixed paraffin-embedded samples using the p95 VeraTag® assay (Monogram Biosciences), which is specific for the active M611 form of p95. Quantitative total HER2 protein expression was measured using the HERmark® assay (Monogram Biosciences). p95 and HERmark cutoffs were pre-specified (Duchnowska, Clin Cancer Res, 20:2805, 2014 and Huang, Am J Clin Pathol, 134:303, 2010). Analyses with p95 were restricted to samples with confirmed HER2 overexpression by HERmark. All hazard ratios (HR) were stratified by estrogen receptor status and grade.

Results: Consistent with previous training (Sperinde, Clin Cancer Res, 16:4226, 2010) and validation (Duchnowska, Clin Cancer Res, 20:2805, 2014) datasets, subjects treated with trastuzumab experienced a shorter time to progression (TTP) when p95 expression levels were above the cutoff versus below the cutoff (HR = 3.8, p = 0.019). However, only a trend was observed between p95 expression levels and overall survival (HR = 2.2, p = 0.20), possibly due to a lower frequency of events and relatively small sample size. The predictive value of p95 was assessed by determining the benefit of adding trastuzumab to chemotherapy treatment in subsets below and above the p95 cutoff. As expected, patients with p95 below the cutoff experienced significant benefit in TTP from adding trastuzumab (HR = 0.13, p<0.001), whereas patients with p95 above the cutoff experienced less benefit (HR = 0.70, p=0.47). p95 expression level was predictive of trastuzumab response with an interaction p-value of 0.015. The results for OS were similar, however trastuzumab benefit was less distinct between the two groups (interaction p = 0.18); HR = 0.23, p = 0.0013 below the p95 cutoff versus HR = 0.50, p = 0.14 above the p95 cutoff.

Conclusions: In this dataset, quantitative p95 expression was predictive of trastuzumab treatment benefit in MBC. Patients with high p95 expression may be particularly good candidates for dual HER2 blockade, as reported in the NeoALTTO trial (Scaltriti, Clin Cancer Res, 21:569, 2015), or other additional therapies.

Citation Format: Sperinde J, Bachmeier B, Weidler JM, Lie Y, Chenna A, Winslow J, Engel J, Schubert-Fritschle G, Sommerhoff C, Petropoulos C, Bates M, Huang W, Nerlich A. Quantitative p95HER2 protein expression is predictive of trastuzumab response in HER2-positive metastatic breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-09.

Abstract P6-11-07: Quantitative p95HER2 levels in primary breast cancers and in matched brain metastases

Background: Patients with HER2-positive breast cancer are at high risk for brain metastases. A large number of HER2-positive tumors also express p95HER2 (p95), a truncated form of HER2 that lacks the trastuzumab binding site but retains kinase activity. Although p95 expression in primary breast tumors is well studied, the prevalence and significance of p95 expression in brain metastases is unknown. In the current study we examined expression of p95 in brain metastases and in matched primary breast tumors.

Methods: Seventy-five pairs of formalin-fixed paraffin-embedded samples from matched primary breast cancers and brain metastases were assayed for quantitative p95 protein expression using the p95 VeraTag® assay (Clin Cancer Res, 16:4226, 2010) specific for the M611 form of p95. Sufficient material to obtain p95 data in both primary and matched brain metastasis samples was available in 52 cases. In the remaining 23 cases, a p95 measurement was obtained in either the primary or brain metastasis sample. Estrogen (ER) and progesterone (PR) receptor status were scored using immunohistochemistry. Hormone receptor positivity was defined as either ER or PR positive. Quantitative HER2 protein expression was measured using the HERmark® assay. Both the p95 VeraTag assay and the HERmark assay measure tumor-averaged protein expression in units of relative fluorescence per mm2 tumor (RF/mm2). Measurements of p95 > 2.8 RF/mm2 and HER2 > 17.8 RF/mm2 were considered as positive results.

Results: There was a net increase in p95 expression in brain metastases relative to the matched primary tumor with a median increase of 1.5-fold (p = 0.001, range 0.2-fold to 35-fold). The increase in p95 expression was only weakly correlated with the increase in quantitative HER2 expression (R2 = 0.18; p = 0.0018). Cases with HERmark-positive tumors were more likely to have the largest (≥ 5-fold) increase in p95 expression compared to those with lower HER2 expression (odds ratio = 6.3; p = 0.018). Changes in p95 levels from primary to brain metastasis were unrelated to hormone receptor status (p = 0.59). P95 positivity in the primary tumor correlated with time from breast cancer diagnosis to first progression (HR = 2.2; p = 0.012) when stratified by hormone receptor status and tumor grade. Although there was a trend towards correlation of p95 positivity in the brain metastasis with time from diagnosis to brain metastasis (HR = 1.7; p = 0.058, stratified as above), p95 positivity did not correlate with overall survival from the time of brain metastasis diagnosis (HR = 1.3; p = 0.42, stratified as above).

Conclusions: This is the first study of quantitative p95 expression in matched primary tumors and brain metastases. Brain metastases of breast cancer show significant increases in p95 protein expression compared to matched primary tumors. These data provide a rationale for future correlative studies on p95 levels in brain metastases.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-11-07.

The ERB family receptor dimerization in glioblastoma—An eTag assay analysis of 23 cases

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Background: Glioblastoma is the most malignant astrocytic tumor and accounts for about 50–60% of all astrocytic neoplasms. Despite intensive radiation and chemotherapy, less than 2% of patients survive more than 3 years. The Erb family of signaling molecules are transmembrane receptors with intrinsic kinase activity (except ErbB3) capable of modifying tyrosine residues on the receptor itself as well as on downstream signaling molecules. Under physiological conditions a variety of ligands interact and act as driving forces in the formation of homo and heterodimeric complexes between the four receptors leading to signal amplification and downstream activities. More than one third of glioblastoma cases show gene amplification of epidermal growth factor receptor (EGFR) which can be in truncated or rearranged form. The eTag assay system (Monogram) is an antibody based fluorescent assay that has the potential to assess the activation state of the EGFR signaling pathway. Methods: Twenty three cases of glioblastoma were selected for eTag analysis. There were twelve males and eleven females with ages ranging from 20–84 years. After reviewing the histology, 10 micron sections were cut from formalin fixed paraffin embedded (FFPE) tumor tissue blocks. Specific monoclonal antibodies of the Erb family bound to a fluorescent reporter (eTag) were applied to tissue sections. After binding of specific analyte, a second monoclonal antibody is added which acts as molecular scissors resulting in cleavage of “eTags”. The released eTag molecules are separated by capillary electrophoresis and measured as relative fluorescent units. Various FFPE tumor cell lines were used as controls. Results: Nineteen out of twenty three tumors (82%) showed the presence of dimers of the Erb family signaling pathway. High levels of intra and /or extracellular EGFR homodimers (HER-1-HER-1) were detected in eight samples (35%). EGFR-HER-3 dimers and EGFR-HER-2 dimers were seen at high levels in four and six samples (17% and 26% respectively). High levels of HER-2-HER3 dimers were detected in six samples (26%). Conclusion: The EGFR signaling pathway plays a substantial role in tumorigenesis of glioblastoma. Identification of receptor homo and heterodimers may be of value during treatment planning of individual patients.

No significant financial relationships to disclose.

Synthesis of 8-(hydroxymethyl)-3,N(4)-etheno-2'-deoxycytidine, a potential carcinogenic glycidaldehyde adduct, and its site-specific incorporation into DNA oligonucleotides

The previously unreported glycidaldehyde adduct, 8-(hydroxymethyl)-3, N(4)-etheno-2'-deoxycytidine (8-HM-epsilondC), has been synthesized for the first time by reaction of 2'-deoxycytidine with bromoacetaldehyde at pH 4.5, followed by reduction with sodium borohydride. The adduct was characterized by UV, MS, and NMR. The compound was stable to neutral and acidic conditions but not in alkaline solution. The corresponding phosphoramidite was synthesized in good yield from the intermediate, 3, N(4)-ethenocarbaldehyde-2'-deoxycytidine, using the standard methodology and site-specifically incorporated in both 15- and 25-mer oligonucleotides, for studies on biochemical and biophysical properties. The resulting oligonucleotides were purified using HPLC, and the base composition was verified by HPLC after enzymatic digestion.

Synthesis of para-benzoquinone and 1,3-bis(2-chloroethyl)nitrosourea adducts and their incorporation into oligonucleotides

Benzene is a widely known carcinogen and a cause of bone-marrow toxicity and leukaemia in humans. para-Benzoquinone is a stable metabolite of benzene. Its reaction with deoxycytidine, deoxyadenosine and deoxyguanosine produces the major stable exocyclic compounds (3-hydroxy)-1,N4-benzetheno-2'-deoxycytidine, (9-hydroxy)-1,N6-benzetheno-2'-deoxyadenosine and (7-hydroxy)-1,N2-benzetheno-2'-deoxyguanosine, respectively, on a large scale and at high yield. The desired products were identified by fast atom bombardment-mass spectrometry, proton nuclear magnetic resonance and UV spectroscopy. These adducts were converted to the fully protected phosphoramidites and incorporated site-specifically into a series of oligonucleotides. 1,N6-Ethano-2'-deoxyadenosine is one of the exocyclic adducts formed during DNA reaction with the antitumour agent, 1,3-bis(2-chloroethyl)nitrosourea. This compound was synthesized on a large scale with a high yield (62%) and then was converted to the phosphoramidite and incorporated site-specifically into oligonucleotides. The coupling efficiency of the incorporation of all these adducts was high (> or = 93%). After de-protection and purification of these oligomers, enzymatic hydrolysis and analysis by high-performance liquid chromatography confirmed the presence of the adduct in the oligomers. These oligomers are being used to investigate the biochemical and physical properties of these adducts.

Differential cleavage of oligonucleotides containing the benzene-derived adduct, 1,N6-benzetheno-dA, by the major human AP endonuclease HAP1 and Escherichia coli exonuclease III and endonuclease IV

We report here that the newly synthesized DNA adduct, 1,N6-benzetheno-dA (pBQ-dA), in defined oligonucleotides [Chenna and Singer, Chem. Res. Toxicol., 8, 865-874], is a substrate for the major human AP endonuclease, HAP1, and the Escherichia coli AP endonucleases, exonuclease III and endonuclease IV. The mechanism of cleavage is identical to that reported previously for 3,N4-benzetheno-dC (pBQ-dC) and leads to a phosphodiester bond cleavage 5' to the adduct. There are, however, significant differences in the rate of cleavage of this adduct by these enzymes. The two bacterial AP endonucleases are both much more efficient than the human repair enzyme. In addition, using two random oligodeoxynucleotide sequences containing a single pBQ-dA, exonuclease III and endonuclease IV are similarly active, while HAP1 shows a distinct sequence preference of approximately 10-fold in efficiency of cleavage. The repair of this adduct by the three recombinant enzymes is further confirmed by using both active site mutant HAP1 proteins and by E.coli mutant strains lacking exonuclease III and/ or endonuclease IV. This sequence-dependent repair of pBQ-dA by HAP1 may play an important role in modulating benzene-induced carcinogenesis.

A single cyclic p-benzoquinone adduct can destabilize a DNA oligonucleotide duplex

p-Benzoquinone (p-BQ), a stable metabolite of the human carcinogen benzene, forms two-ring benzetheno exocyclic base adducts with C, A, and G bases in DNA. As a part of a project for studying the biological effect of the p-BQ adducts, we report here on the first biophysical characterization of oligodeoxyribonucleotide duplexes containing a single site-specific p-BQ-C, using thermal denaturation and circular dichroism (CD). We find that the thermal and thermodynamic stabilities of the control duplex are reduced by p-BQ-C. The Tm value decreases by 12.6 degrees C at the duplex concentration of 1.5 microM and the Delta G o by 10.2 kcal/mol. The latter was determined from the concentration dependence of the Tm values. The destabilization has little dependence on the nature of the opposite base. This reduction is higher than that of the single base mismatches studied (-4.9 to -7.9 kcal/mol) and is close to that observed with an adjacent double mismatch-containing duplex (-11.3 kcal/mol). The overall B-conformation of the duplex with a p-BQ-C is, however, only slightly altered, relative to the parent duplex, as shown by CD spectra. The p-BQ-C-containing duplex has been found recently to be a good substrate for the major human AP endonuclease as compared to an abasic site-containing duplex [Hang, B., et al. (1997) Biochemistry 36, 15411-15418]. We now find that the thermodynamic properties and the localized conformational changes of a p-BQ-C-containing duplex are apparently related to those reported for a duplex containing an abasic site.

Sequence context is an important determinant in the mutagenic potential of 1,N6-ethenodeoxyadenosine (epsilonA): formation of epsilonA basepairs and elongation in defined templates

Many laboratories have obtained data on mutagenicity of modified bases in naturally occurring DNA sequences. It has often been noted that mutation is favored in certain sequence contexts, sometimes termed 'hot spots'. This approach to the contribution of neighboring sequences does not permit a systematic study of both the qualitative and quantitative mutational frequencies. In the present experiments we have chosen to use the exocyclic adduct, 1,N6-etheno A (epsilonA), site-specifically placed in a defined 25-mer oligonucleotides in which epsilonA is flanked by differing 5' and 3' tandem bases. Mutation was assessed using an in vitro replication assay and five polymerases of varying fidelity. The relevant central sequences were 3' --> 5' -CC-epsilonA-CC-, -GG-epsilonA-GG-, -TT-epsilonA-TT-, -AA-epsilonA-AA-, -GG-epsilonA-TT-, -TT-epsilonA-AA-, -AT-epsilonA-TT- and -TA-epsilonA-TA-. Using the Klenow fragment (Kf) (exo+ or exo-) of E. coli Pol I, it was found the epsilonA is an ambiguous base and, with varying efficiencies, all four dNTPs could be inserted opposite epsilonA in all sequences. However, only 3' --> 5' -TT-epsilonA-TT-, -GG-epsilonA-TT- and -AT-epsilonA-TT- were fully extended to a significant extent. The only sequences essentially blocked at the position of epsilonA were -AA-epsilonA-AA- and -TT-epsilonA-AA-. The others were intermediate. When replication was performed with Sequenase, MMLV RT or HIV RT, different patterns were observed, in which replication terminated one base prior to epsilonA, at epsilonA, or one base after epsilonA without further extension. In favored sequences, using the Klenow fragment, an epsilonA x N pair could be extended to form normal basepairs. No extension could be demonstrated in sequences in which tandem adenines were 5' to epsilonA. Kinetic data showed that two of the epsilonA x N pairs, epsilonA x A and epsilonA x C, could form at 10 microM or less dNTP. Which bases were preferentially inserted opposite epsilonA was a function of the flanking bases. Under the kinetic conditions used, epsilonA x T did not form even at 1 mM dTTP. These results indicate that the chemical structure of an adduct is not the only determinant of mutagenic efficiency. It is likely that the effect of the adduct on replication is due to the changes in the structural environment conferred by the flanking bases.

Synthesis of a benzene metabolite adduct, 3"-hydroxy-1,N2-benzetheno-2'-deoxyguanosine, and its site-specific incorporation into DNA oligonucleotides

p-Benzoquinone (p-BQ) is a stable metabolite of benzene and a number of other drugs and chemicals. 2'-Deoxyguanosine was allowed to react with p-BQ in aqueous solution (pH 4.5, 7.4, and 9.3). At pH 7.4 and 9.3 one major product was found in low yield; at pH 4.5 no product was detected. In nonaqueous conditions (DMF or DMSO, in the presence of K2CO3), an unstable intermediate with two p-BQ moieties was found which slowly converted to the product formed in aqueous solution. These products were isolated by silica gel, column chromatography, or reverse-phase HPLC and characterized by UV, 1H NMR, FAB-MS, and electrospray MS. The major stable product of the reaction of dG with p-BQ is an exocyclic compound. 3"-hydroxy-1,N2-benzetheno-2'-deoxyguanosine (p-BQ-dG). Incorporation of the adduct into oligonucleotides requires the protection of three hydroxyl groups (C7, 5', 3') and the amino group at N5. The exocyclic hydroxyl and the amino group were protected by acylation after protecting the 5'-and the 3'-hydroxyl groups of the sugar moiety by 4,4'-dimethoxytrityl and a cyanoethyl N,N-diisopropylphosphoramidite group, respectively. This is the first time the fully protected phosphoramidite of p-BQ-dG has been prepared and used in the synthesis of site specifically modified oligonucleotides. After deprotection with 1,3-diazabicyclo[5.4.0]undec-7-ene (DBU), in ethanol, oligomers purified by gel electrophoresis and HPLC. Enzymatic hydrolysis and analysis by HPLC confirmed the presence of p-BQ-dG in the oligomers. These oligomers are now under investigation for their biochemical properties.

An unusual mechanism for the major human apurinic/apyrimidinic (AP) endonuclease involving 5' cleavage of DNA containing a benzene-derived exocyclic adduct in the absence of an AP site

The major human apurinic/apyrimidinic (AP) endonuclease (class II) is known to cleave DNA 5' adjacent to an AP site, which is probably the most common DNA damage produced hydrolytically or by glycosylase-mediated removal of modified bases. p-Benzoquinone (pBQ), one of the major benzene metabolites, reacts with DNA to form bulky exocyclic adducts. Herein we report that the human AP endonuclease directly catalyzes incision in a defined oligonucleotide containing 3,N4-benzetheno-2'-deoxycytidine (pBQ-dC) without prior generation of an AP site. The enzyme incises the oligonucleotide 5' to the adduct and generates 3'-hydroxyl and 5'-phosphoryl termini but leaves the pBQ-dC on the 5' terminus of the cleavage fragment. The AP function of the enzyme is not involved in this action, as no preexisting AP site is present nor is a DNA glycosylase activity involved. Nicking of the pBQ-dC adduct also leads to the same "dangling base" cleavage when two Escherichia coli enzymes, exonuclease III and endonuclease IV, are used. Our finding of this unusual mode of action used by both human and bacterial AP endonucleases raises important questions regarding the requirements for substrate recognition and catalytic active site(s) for this essential cellular repair enzyme. We believe this to be the first instance of the presence of a bulky carcinogen adduct leading to this unusual mode of action.

Replication of O4-methylthymine-containing oligonucleotides: effect of 3' and 5' flanking bases on formation and extension of O4-methylthymine . guanine basepairs

Four 25-mer oligonucleotides containing m4T(T*) with the 3'-->5' sequences A-T*-A, A-T*-C, G-T*-G and G-T*-C, together with four oligonucleotides containing the same sequences with unmodified T, were studied for the effect of the immediate 5' and 3' bases flanking m4T on in vitro replication. Under enzyme-limiting conditions, all m4T-containing oligomers showed a varying sequence-dependent blockage at the base 3' to m4T. However, with time and high concentrations of dNTP's, full replication beyond m4T did occur with Klenow fragment (Kf), although substantial blockage remained, particularly in the case when the sequence was 3'-A-T*-A-5'. The extent of blockage at the base 3' to m4T, compared to complete replication using Kf, followed the order A-T*-A > A-T*-C >> G-T*-C > or = G-T*-G. Two other DNA polymerases, HIV-RT and Sequenase, which, unlike Kf, do not have 3' proofreading activity differ, agreed with data obtained with Kf. We conclude that the extent of complete replication of m4T-containing oligomers is primarily a function of the 3' flanking base with a lesser effect of the 5' base and requires specific dGTP insertion opposite m4T. These data suggest that a 5' G . C pair favors the formation of the following T*-G and this latter step is rate-limiting. However, once a T*-G pair is formed, rapid elongation to full length transcripts occurs.

1,N6-ethenoadenine and 3,N4-ethenocytosine are excised by separate human DNA glycosylases

We previously reported our finding that human cells contain glycosylase activity toward all four etheno bases formed in DNA by chloroacetaldehyde and related bi-functional aldehydes. By enzyme purification, including FPLC, we isolated two separate glycosylase activities for 1,N6-ethenoadenine (epsilon A) and for 3,N4-ethenocytosine (epsilon C) respectively, from crude HeLa cell-free extracts, which also contained a number of well-described glycosylases. When Mono-S FPLC purified proteins were assayed against defined oligomers containing either epsilon A or epsilon C, it was found that epsilon A and epsilon C glycosylases were completely separated. It could also be demonstrated that each enzyme bound to and cut only epsilon A- or epsilon C-containing oligomers respectively. There was no overlap in specificity for these two substrates. Several other human glycosylase substrates were also tested and none were cleaved by epsilon C glycosylase. The epsilon C glycosylase activity identified in the present study apparently represents a previously unknown glycosylase. This work also suggests that enzyme recognition of closely related DNA adducts may depend upon subtle changes in local conformation.

Large scale synthesis of p-benzoquinone-2'-deoxycytidine and p-benzoquinone-2'-deoxyadenosine adducts and their site-specific incorporation into DNA oligonucleotides

Benzene is a carcinogen in rodents and a cause of bone marrow toxicity and leukemia in humans. p-Benzoquinone (p-BQ) is one of the stable metabolites of benzene, as well as of a number of drugs and other chemicals. 2'-Deoxycytidine (dC) and 2'-deoxyadenosine (dA) were allowed to react with p-BQ in aqueous solution at pH 7.4 and 4.5. The yields were considerably higher at pH 4.5 than at pH 7.4, as indicated by HPLC analysis. The desired products were isolated by column chromatography on silica gel or cellulose. Identification was done by FAB-MS, 1H NMR, and UV spectroscopy. The reaction of p-BQ with dC and dA at pH 4.5 produced the exocyclic compounds 3-hydroxy-1,N4-benzetheno-2'-deoxycytidine (p-BQ-dC), and 9-hydroxy-1,N6-benzetheno-2'-deoxyadenosine (p-BQ-dA), respectively, in a large scale and high yield. These adducts have been previously made in a microgram scale as the 3'-phosphate for 32P-postlabeling studies of their incidence in DNA. The p-BQ-dC and p-BQ-dA adducts have, in addition to the two hydroxyl groups of deoxyribose, one newly formed hydroxyl group at the C-3 or C-9 of the exocyclic base of each product respectively. Incorporation of these adducts into oligonucleotides as the phosphoramidite requires the protection of all three hydroxyl groups in these compounds. The exocyclic hydroxyl on the base has been successfully protected by acylation after protecting the 5'- and the 3'-hydroxyl groups of the sugar moiety with a 4,4'-dimethoxytrityl group and a cyanoethyl N,N-diisopropylphosphoramidite group, respectively. For the first time, to our knowledge, the fully protected phosphoramidites of p-BQ-dC and p-BQ-dA were prepared and incorporated site-specifically into a series of oligonucleotides. The coupling efficiency was very high (> 98%). However, deprotection of the DNA oligomers with ammonia produced only 50% of the desired oligomers containing the adduct. In contrast, when 10% of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in methanol at room temperature was used, only the desired oligomers were detected by HPLC. Thus, by deprotecting the oligomers with methoxide ions (DBU/methanol) and avoiding the use of ammonia, a high yield of modified DNA was obtained. After purification of these oligomers by HPLC, they were hydrolyzed enzymatically and analyzed by HPLC, which confirmed the base composition and the incorporation of the adducts. The mass spectroscopic analysis of the DNA oligomers was confirmed by electrospray MS. These oligomers are now under investigation for their biochemical properties.

The benzene metabolite p-benzoquinone forms adducts with DNA bases that are excised by a repair activity from human cells that differs from an ethenoadenine glycosylase

Benzene is a ubitiquous human environment mental carcinogen. One of the major metabolites is hydroquinone, which is oxidized in vivo to give p-benzoquinone (p-BQ). Both metabolites are toxic to human cells. p-BQ reacts with DNA to form benzetheno adducts with deoxycytidine, deoxyadenosine, and deoxyguanosine. In this study we have synthesized the exocyclic compounds 3-hydroxy-3-N4-benzetheno-2'-deoxycytidine (p-BQ-dCyd) and 9-hydroxy-1,N6-benzetheno-2'-deoxyadenosine (p-BQ-dAdo), respectively, by reacting deoxycytidine and deoxyadenosine with p-BQ. These were converted to the phosphoamidites, which were then used to prepare site-specific oligonucleotides with either the p-BQ-dCyd or p-BQ-dAdo adduct (pbqC or pbqA in sequences) at two different defined positions. These oligonucleotides were efficiently nicked 5' to the adduct by partially purified HeLa cell extracts--the pbqC-containing oligomer more rapidly than the pbqA-containing oligomer. In contrast to the enzyme binding to derivatives produced by the vinyl chloride metabolite chloroacetaldehyde, the oligonucleotides up to 60-mer containing p-BQ adducts did not bind measurably to the same enzyme preparation in a gel retardation assay. Furthermore, there was no competition for the binding observed between oligonucleotides containing 1,N6-etheno A deoxyadenosine (1,N6-etheno-dAdo; epsilon A in sequences) and these oligomers containing either of the p-BQ adducts, even at 120-fold excess. When highly purified fast protein liquid chromatography (FPLC) enzyme fractions were obtained, there appeared to be two closely eluting nicking activities. One of these enzymes bound and cleaved the epsilon A-containing deoxyoligonucleotide. The other enzyme cleaved the pbqA- and pbqC-containing deoxyoligonucleotides. One additional unexpected fact was that bulk p-BQ-treated salmon sperm DNA did compete effectively with the epsilon A-containing oligonucleotide for protein binding. This raises the possibility that such DNA contains other, as-yet-uncharacterized adducts that are recognized by the same enzyme that recognizes the etheno adducts. In summary, we describe a previously undescribed human DNA repair activity, possibly a glycosylase, that excises from DNA pbqC and pbqA, exocyclic adducts resulting from reaction of deoxycytidine and deoxyadenosine with the benzene metabolite, p-BQ. This glycosylase activity is not identical to the one previously reported from this laboratory as excising the four etheno bases from DNA.

All four known cyclic adducts formed in DNA by the vinyl chloride metabolite chloroacetaldehyde are released by a human DNA glycosylase

We have previously reported that human cells and tissues contain a 1,N6-ethenoadenine (epsilon A) binding protein, which, through glycosylase activity, releases both 3-methyladenine (m3A) and epsilon A from DNA treated with methylating agents or the vinyl chloride metabolite chloroacetaldehyde, respectively. We now find that both the partially purified human epsilon A-binding protein and cell-free extracts containing the cloned human m3A-DNA glycosylase release all four cyclic etheno adducts--namely epsilon A, 3,N4-ethenocytosine (epsilon C), N2,3-ethenoguanine (N2,3-epsilon G), and 1,N2-ethenoguanine (1,N2-epsilon G). Base release was both time and protein concentration dependent. Both epsilon A and epsilon C were excised at similar rates, while 1,N2-epsilon G and N2,3-epsilon G were released much more slowly under identical conditions. The cleavage of glycosyl bonds of several heterocyclic adducts as well as those of simple methylated adducts by the same human glycosylase appears unusual in enzymology. This raises the question of how such a multiple, divergent activity evolved in humans and what may be its primary substrate.

Characterization of 2'-deoxycytidine and 2'-deoxyuridine adducts formed in reactions with acrolein and 2-bromoacrolein

The products of the reaction of the mutagenic aldehydes, acrolein and 2-bromoacrolein, with 2'-deoxycytidine and 2'-deoxyuridine have been determined. These products, formed at physiological conditions, were isolated by reverse-phase HPLC and characterized by UV, 1H NMR, fast atom bombardment MS, electrospray MS, and chemical transformation. The reaction of 2'-deoxycytidine with acrolein and 2-bromoacrolein produced the exocyclic compounds 3-(2'-deoxyribosyl)-7,8,9-trihydro-7-hydroxypyrimido[3,4- c]pyrimidin-2-one and 3-(2'-deoxyribosyl)-7,8,9-trihydro-7-hydroxy-8-bromopyrimido [3,4-c] pyrimidin-2-one, respectively. In addition to the chiral centers of deoxyribose, one new chiral center was formed from C-1 of acrolein and two new chiral centers were formed from C-1 and C-2 of 2-bromoacrolein, creating a mixture of diastereomers for each product. These compounds are not stable in basic solution and undergo ring opening and hydrolytic deamination, resulting in 2'-deoxyuridine adducts. The N3-alkylated 2'-deoxyuridines were also synthesized by permitting 2'-deoxyuridine to react with 2-bromoacrolein and acrolein. An unstable intermediate, N3-(2"-bromo-3"-oxopropyl)-2'-deoxyuridine, was also isolated and characterized from the reaction with 2-bromoacrolein. The reaction of 2'-deoxyuridine with acrolein gave N3-(3"-oxopropyl)-2'-deoxyuridine as the major product, which was reduced to its corresponding alcohol with NaBH4. Reactions of 2'-deoxycytidine with 2-bromoacrolein and acrolein proceed most rapidly at acidic or neutral pH; however, 2'-deoxyuridine reacts most rapidly at neutral or basic pH.

Characterization of thymidine adducts formed by acrolein and 2-bromoacrolein

Thymidine was permitted to react with the known mutagens acrolein and 2-bromoacrolein under physiological conditions. The products of these reactions were separated by HPLC and characterized by UV, FAB/MS, electrospray MS, 1H NMR and chemical transformation. The reaction with acrolein gave one major product, N3-(3''-oxopropyl)thymidine, which is unstable in aqueous solution and was reduced with sodium borohydride to the corresponding alcohol. Reaction with 2-bromoacrolein yielded the unstable intermediate, N3-(2''-bromo-3''-oxopropyl)thymidine, and two stable products, the diastereomers of N3-(2''-hydroxy-3''-oxopropyl)thymidine, which are slowly transformed to N3-(2''-oxo-3''-hydroxypropyl)thymidine. Reactions with both mutagens proceed most rapidly at pH 9.2, less rapidly at pH 7.4, and no products are found at pH 4.2. Stable adducts found in the reaction of 2-bromoacrolein were also identified in reactions with single-strand oligodeoxynucleotides using a sensitive, selected ion monitoring GC/MS procedure.