CTDSP1 inhibitor rabeprazole regulates DNA-PKcs dependent topoisomerase I degradation and irinotecan drug resistance in colorectal cancer

Irinotecan specifically targets topoisomerase I (topoI), and is used to treat various solid tumors, but only 13–32% of patients respond to the therapy. Now, it is understood that the rapid rate of topoI degradation in response to irinotecan causes irinotecan resistance. We have published that the deregulated DNA-PKcs kinase cascade ensures rapid degradation of topoI and is at the core of the drug resistance mechanism of topoI inhibitors, including irinotecan. We also identified CTD small phosphatase 1 (CTDSP1) (a nuclear phosphatase) as a primary upstream regulator of DNA-PKcs in response to topoI inhibitors. Previous reports showed that rabeprazole, a proton pump inhibitor (PPI) inhibits CTDSP1 activity. The purpose of this study was to confirm the effects of rabeprazole on CTDSP1 activity and its impact on irinotecan-based therapy in colon cancer. Using differentially expressing CTDSP1 cells, we demonstrated that CTDSP1 contributes to the irinotecan sensitivity by preventing topoI degradation. Retrospective analysis of patients receiving irinotecan with or without rabeprazole has shown the effects of CTDSP1 on irinotecan response. These results indicate that CTDSP1 promotes sensitivity to irinotecan and rabeprazole prevents this effect, resulting in drug resistance. To ensure the best chance at effective treatment, rabeprazole may not be a suitable PPI for cancer patients treated with irinotecan.

Camptothecin resistance is determined by the regulation of topoisomerase I degradation mediated by ubiquitin proteasome pathway

Proteasomal degradation of topoisomerase I (topoI) is one of the most remarkable cellular phenomena observed in response to camptothecin (CPT). Importantly, the rate of topoI degradation is linked to CPT resistance. Formation of the topoI-DNA-CPT cleavable complex inhibits DNA re-ligation resulting in DNA-double strand break (DSB). The degradation of topoI marks the first step in the ubiquitin proteasome pathway (UPP) dependent DNA damage response (DDR). Here, we show that the Ku70/Ku80 heterodimer binds with topoI, and that the DNA-dependent protein kinase (DNA-PKcs) phosphorylates topoI on serine 10 (topoI-pS10), which is subsequently ubiquitinated by BRCA1. A higher basal level of topoI-pS10 ensures rapid topoI degradation leading to CPT resistance. Importantly, PTEN regulates DNA-PKcs kinase activity in this pathway and PTEN deletion ensures DNA-PKcs dependent higher topoI-pS10, rapid topoI degradation and CPT resistance.

Developing a Phosphospecific IHC Assay as a Predictive Biomarker for Topoisomerase I Inhibitors

Phosphorylation is the most extensively studied posttranslational modification of proteins. There are approximately 500 kinases known in the human genome. The kinase-activated pathways regulate almost every aspect of cell function and a deregulated kinase cascade leads to impaired cellular function. Impaired regulation of several kinase cascades, including the epidermal growth factor receptor (EGFR) pathway, leading to tumor pathogenesis, is well documented. Thus, a phosphospecific test with prognostic or predictive value was expected in oncology. However, no phosphospecific IHC test is used in oncology clinics. Human topoisomerase I (topoI) inhibitors, camptothecin and its analogues (CPT), are used extensively to treat various solid tumors. Depending on tumor type, the response rate is only 13-32%. We have demonstrated that the deregulated kinase cascade is at the core of CPT resistance. DNA-PKcs, a kinase central to the DNA-double-strand break (DSB) response pathway, phosphorylates topoI at serine 10 (topoI-pS10), and cells with higher basal levels of topoI-pS10 degrade topoI rapidly and are resistant to this class of drug. The higher basal level of topoI phosphorylation is due to continual activation of DNA-PKcs, and one potential mechanism of this pathway activation is failure of upstream effector phosphatases such as phosphatase and tensin homolog (PTEN). Based on this understanding, we have developed an IHC-based test (P-topoIDx) that can stratify the responder and non-responder patient population.

Abstract 4653: DNA-PKcs dependent phosphorylation of topoI-S10 determines its ubiquitination by BRCA1/BARD1, rate of topoI degradation and CPT response

Abstract: The age-adjusted mortality rate for cancer is about the same in the 21st century as it was 50 years ago. In the past decade, our understanding of oncogenesis at molecular level has increased greatly. This has resulted in the development of several targeted drugs and many more are in the pipeline. However, the lack of predictive biomarkers to stratify the patient population has restricted the benefits of these new developments. Camptothecins (CPTs) target topoisomeraseI (topoI) and represent a highly potent class of anticancer drugs. Two topoI inhibitors, topotecan and irrinotecan (CPT analogues), are in clinical use and several other topoI inhibitors are in different phases of development. SCLC, colon, ovarian, breast and cervical carcinomas are treated with topoI inhibitors. However, only 13% to 32% of patients respond to these drugs. TopoI mutations are rare in the patient population, and CPTs are not substrates for MDR transporters, therefore the rate of proteolytic degradation of topoI is a potential mechanism explaining CPT resistance. A differential rate of topoI degradation by the ubiquitin-proteosomal pathway (UPP) has been linked to CPT response, but the mechanism is not well understood. Using a functional proteomics approach, we have isolated a topoI interacting complex and have determined that: i) Ku70/Ku80/DNA-PKcs associates with topoI, and DNA-PKcs specifically phosphorylates topoI at S10, ii) S10-phosphorylated topoI is ubiquitinated by the BRCA1/BARD1 heterodimer, K-48 ubiquitin linkage indicates polyubiquitination and proteosomal degradation of topoI in response to CPT, iii) topoI S10 phosphorylation level determines the rate of topoI ubiquitination and proteosomal degradation in triple negative breast cancer (TNBC) and colon cancer cells. Higher levels of topoI pS10 ensures rapid degradation of topoI by the UPP and confers resistance to CPT. These cell based findings have further been tested in retrospective clinical studies. We have raised a monoclonal phosphospecific antibody against topoI-pS10 and shown its specificity in IF and IHC assays. In a retrospective study, we have performed IHC of FFPE tissues from metastatic CRC patients treated with FOLFIRI (combination therapy, 5FU, Leucovorin and Irinotecan). IHC analysis was performed in ten responders and ten non-responders tissues by anti topoI-pS10. Our preliminary data indicates that non-responders have very high level of topoI-pS10; in contrast the responders were negative for IHC staining. A larger retrospective study is underway to develop this predictive biomarker.

Citation Format: Ankur K. Shah, Vibhu Sachdev, Julian Taylor Parker, Yevnegyia Malinkovich, Yara Hamade Tohme, Yiheng Hu, Jeffrey D. Parvin, Ajit K. Bharti. DNA-PKcs dependent phosphorylation of topoI-S10 determines its ubiquitination by BRCA1/BARD1, rate of topoI degradation and CPT response. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4653. doi:10.1158/1538-7445.AM2013-4653

Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

Mutants of Arabidopsis as tools to understand the regulation of phenylpropanoid pathway and UVB protection mechanisms

Plants accumulate certain phenylpropanoid compounds in the vacuoles of their epidermal and subepidermal cell layers thereby protecting the underlying tissue against UVB-induced damage. However, a number of mutants of Arabidopsis thaliana are known that fail to synthesize these protective pigments, thereby allowing harmful UVB radiation to penetrate into their dermal layers. Study of several of these nonlethal mutants, defective in various aspects of flavonoid and lignin biosynthesis, has led to a better understanding of the coordinate regulation and expression of important genes as well as of mechanisms involved in plant defense against UVB radiation. The characteristics of the various phenylpropanoid mutants of Arabidopsis, viz. flavonoid mutants (banyuls [ban]; increased chalcone synthase expression 1 [icx1]; transparent testa [tt] and ultraviolet sensitive [uvs]) and hydroxycinnamic acid ester mutants (ferulic acid hydroxylase 1 [fah1] and sinapoylglucose accumulator 1 [sng1]) are discussed in detail. We have briefly touched upon, wherever relevant, the unique aspects in other plant species too.

Involvement of amino acids 361 to 364 of human topoisomerase I in camptothecin resistance and enzyme catalysis

Camptothecins are antineoplastic drugs that specifically target the enzyme DNA topoisomerase I. Prior work has identified a human topoisomerase I mutation, F361S, that confers resistance to camptothecin. We now demonstrate that substitutions in the 361-364 region can alter DNA cleavage/ligation by the enzyme. The defective catalysis exhibited by certain mutants likely relates to an impaired interaction with DNA, since these enzymes are more sensitive to the inhibitory effects of DNA binding ligands. Moreover, studies with peptides and fusion proteins suggest that the 361-364 region may bind DNA directly. The finding that the 361-364 region is involved in both enzyme catalysis and camptothecin resistance suggests that this region is part of the active site of human topoisomerase I and that camptothecin may interact with the enzyme at this site.

Identification of a nucleolin binding site in human topoisomerase I

DNA topoisomerase I (topo I) is involved in the regulation of DNA supercoiling, gene transcription, and rDNA recombination. However, little is known about interactions between topo I and other nuclear proteins. We used affinity chromatography with a topo I fusion protein to screen U-937 leukemic cell extracts and have identified nucleolin as a topo I-binding protein. Coimmunoprecipitation and other studies demonstrate that the interaction between topo I and nucleolin is direct. Furthermore, deletion analyses have identified the 166-210-amino acid region of topo I as sufficient for the interaction with nucleolin. Since nucleolin has been implicated in nuclear transport and in a variety of transcriptional processes, the interaction with topo I may relate to the cellular localization of topo I or to the known role of this topoisomerase in transcription.