Epigenetic and genetic inactivation of tyrosyl-DNA-phosphodiesterase 1 (TDP1) in human lung cancer cells from the NCI-60 panel

Abstract

Tyrosyl-DNA-phosphodiesterase 1 (TDP1) repairs 3’-blocking DNA lesions by catalytically hydrolyzing the tyrosyl-DNA-phosphodiester bond of trapped topoisomerase I (Top1) cleavage complexes (Top1cc). It also removes 3’-blocking residues derived from oxidative damage or incorporation of chain terminating anticancer and antiviral nucleosides. Thus, TDP1 is regarded as a determinant of resistance to Top1 inhibitors and chain terminating nucleosides, and possibly of genomic stability. In the 60 cell lines of the NCI Developmental Therapeutic Anticancer Screen (the NCI-60), whose whole genome transcriptome and mutations have recently been characterized, we discovered two human lung cancer cell lines deficient for TDP1 (NCI_H522 and HOP_62). HOP_62 shows undetectable TDP1 mRNA and NCI_H522 bears a homozygous deleterious mutation of TDP1 at a highly conserved amino acid residue (K292E). Absence of TDP1 protein and lack of TDP1 catalytic activity were demonstrated in cell lysates from both cell lines. Lack of TDP1 expression in HOP_62 was shown to be due to TDP1 promoter hypermethylation. Our study provides insights into the possible inactivation of TDP1 in cancers and its relationship to cellular response to Top1-targeted drugs. It also reveals two TDP1 knockout lung cancer cell lines for further TDP1 functional analyses.

TDP1 is Critical for the Repair of DNA Breaks Induced by Sapacitabine, a Nucleoside also Targeting ATM- and BRCA-Deficient Tumors

“…In this study, we extend our initial finding that TDP1 was found inactivated in two of the lung cancer cell lines of the NCI-60 (36) by showing lowest TDP1 expression in NSCLC cancer cell lines and tumor samples, and establishing that both gene copy number defects and promoter hypermethylation cause such defective expression. We also found a broad range of expression of TDP1 across cancer cells (Figure 6 and Supplemental Figure 2).…”

“…Moreover, leukemia and blood cancers tend to have high TDP1 expression (Figure 6B) while non-small cell lung cancers (NSCLC) have the broadest TDP1 expression range with some cells having background (no significant) TDP1 expression (Figure 6C and Supplementary Figure 2A). In the NSCLC cell lines, we found that lack of TDP1 expression is also driven by promoter hypermethylation (Figure 6D) (36). …”

Tyrosyl-DNA-phosphodiesterases (TDP1 and TDP2)

“…TDP1 orthologs exist in all organisms and act both in the nucleus and vertebrate mitochondria (where Top1mt is present [42]) [43–46]. Genetic inactivation of TDP1 confers hypersensitivity to camptothecins in human [47–50], murine [51,52], and chicken cells [27,45,53], as well as in Leishmania donovani (trypanosome) [46], and in yeast Saccharomyces pombe [54], and S. cerevisiae [41,55]. …”

“…Because TDP1 or TDP2 knockout vertebrate cells show normal cell growth and knockout mice are viable without obvious phenotype [50–52,132], it is expected that TDP1 or TDP2 inhibitors will be well tolerated.…”

Neuroprotection and repair of 3′-blocking DNA ends by glaikit (gkt) encoding Drosophila tyrosyl-DNA phosphodiesterase 1 (TDP1)

“…This finding was surprising because TDP1 is not essential for viability in other eukaryotes, including yeast (10,11), chicken and human cells (4,24), and mice (16,25). Here we use an insertional mutant (Exelixis line c03958) to elucidate the role of TDP1 in flies and its critical activity for the repair of 3′-blocked DNA termini and neuroprotection.…”