BACKGROUND: Glycosylated proteins play important roles in cell-to-cell interactions, immunosurveillance, and a variety of receptor-mediated and specific protein functions through a highly complex repertoire of glycan structures. Aberrant glycosylation has been implicated in cancer for many years.

Topoisomerase I cleavage complexes can be induced by a variety of DNA damages and by the anticancer drug camptothecin. We have developed a ligation-mediated PCR (LM-PCR) assay to analyze replication-mediated DNA double-strand breaks induced by topoisomerase I cleavage complexes in human colon carcinoma HT29 cells at the nucleotide level. We found that conversion of topoisomerase I cleavage complexes into replicationmediated DNA double-strand breaks was only detectable on the leading strand for DNA synthesis, which suggests an asymmetry in the way that topoisomerase I cleavage complexes are metabolized on the two arms of a replication fork. Extension by Taq DNA polymerase was not required for ligation to the LM-PCR primer, indicating that the 3 DNA ends are extended by DNA polymerase in vivo closely to the 5 ends of the topoisomerase I cleavage complexes. These findings suggest that the replication-mediated DNA double-strand breaks generated at topoisomerase I cleavage sites are produced by replication runoff. We also found that the 5 ends of these DNA double-strand breaks are phosphorylated in vivo, which suggests that a DNA 5 kinase activity acts on the double-strand ends generated by replication runoff. The replication-mediated DNA doublestrand breaks were rapidly reversible after cessation of the topoisomerase I cleavage complexes, suggesting the existence of efficient repair pathways for removal of topoisomerase I-DNA covalent adducts in ribosomal DNA.DNA topoisomerases are ubiquitous enzymes that regulate the topological state of DNA. They participate in essential cellular processes, including replication, transcription, chromosome segregation, and recombination (22,34,71). Eukaryotic DNA topoisomerase I (top1) acts as a monomer, and its catalytic activity can be divided into four steps (61): (i) binding of the enzyme to duplex DNA, (ii) single-stranded DNA cleavage by a transesterification reaction in which a top1 tyrosinehydroxyl group becomes covalently linked to the 3Ј phosphate of a DNA phosphodiester bond to generate a 5Ј-hydroxyl DNA terminus, (iii) DNA relaxation by controlled rotation around the intact DNA strand (61); and (iv) religation of the cleaved DNA by nucleophilic attack from the 5Ј-hydroxyl DNA end and dissociation of the top1 tyrosyl residue from the 3Ј end. The topoisomerase-linked DNA breaks are commonly referred to as cleavage complexes (22,34,71). Under physiological conditions, they are short-lived catalytic intermediates.A number of physiological and environmental DNA modifications can inhibit top1 by inducing top1 cleavage complexes. These include DNA mismatches or abasic sites (37, 48, 73), oxidative base damage (47), base alkylation and carcinogenic adducts (44, 66), UV photoproducts (50, 62), and DNA breaks (11, 45). Trapping of top1 cleavage complexes is also the primary mechanism of action of camptothecin (CPT), a potent anticancer agent which reversibly inhibits the religation step of the top1 catalytic cycle (25,29,39,40). The cytotoxicity of top1 cleavage complexes is atte...

Glycomic profiles derived from human blood sera of 10 healthy males were compared to those from 24 prostate cancer patients. The profiles were acquired using MALDI-MS of permethylated N-glycans released from 10-microL sample aliquots. Quantitative permethylation was attained using solid-phase permethylation. Principal component analysis of the glycomic profiles revealed significant differences among the two sets, allowing their distinct clustering. The first principal component distinguished the 24 prostate cancer patients from the healthy individuals. It was determined that fucosylation of glycan structures is generally higher in cancer samples (ANOVA test p-value of 0.0006). Although more than 50 N-glycan structures were determined, 12 glycan structures, of which six were fucosylated, were significantly different between the two sample sets. Significant differences were confirmed through two independent statistical tests (ANOVA and ROC analyses). Ten of these structures had significantly higher relative intensities in the case of the cancer samples, while the other two were less abundant in the cancer samples. All 12 structures were statistically significant, as suggested by their very low ANOVA scores (<0.001) and ROC analysis, with area under the curve values close to 1 or 0. Accordingly, these structures can be considered as cancer-specific glycans and potential prostate cancer biomarkers. Therefore, serum glycomic profiling appears worthy of further investigation to define its role in cancer early detection and prognostication.