The potential role of Alu Y in the development of resistance to SN38 (Irinotecan) or oxaliplatin in colorectal cancer

BACKGROUND: Irinotecan (SN38) and oxaliplatin are chemotherapeutic agents used in the treatment of colorectal cancer. However, the frequent development of resistance to these drugs represents a considerable challenge in the clinic. Alus as retrotransposons comprise 11% of the human genome. Genomic toxicity induced by carcinogens or drugs can reactivate Alus by altering DNA methylation. Whether or not reactivation of Alus occurs in SN38 and oxaliplatin resistance remains unknown. RESULTS: We applied reduced representation bisulfite sequencing (RRBS) to investigate the DNA methylome in SN38 or oxaliplatin resistant colorectal cancer cell line models. Moreover, we extended the RRBS analysis to tumor tissue from 14 patients with colorectal cancer who either did or did not benefit from capecitabine + oxaliplatin treatment. For the clinical samples, we applied a concept of ‘DNA methylation entropy’ to estimate the diversity of DNA methylation states of the identified resistance phenotype-associated methylation loci observed in the cell line models. We identified different loci being characteristic for the different resistant cell lines. Interestingly, 53% of the identified loci were Alu sequences- especially the Alu Y subfamily. Furthermore, we identified an enrichment of Alu Y sequences that likely results from increased integration of new copies of Alu Y sequence in the drug-resistant cell lines. In the clinical samples, SOX1 and other SOX gene family members were shown to display variable DNA methylation states in their gene regions. The Alu Y sequences showed remarkable variation in DNA methylation states across the clinical samples. CONCLUSION: Our findings imply a crucial role of Alu Y in colorectal cancer drug resistance. Our study underscores the complexity of colorectal cancer aggravated by mobility of Alu elements and stresses the importance of personalized strategies, using a systematic and dynamic view, for effective cancer therapy. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1552-y) contains supplementary material, which is available to authorized users

Impact of Whole Genome Doubling on Detection of Circulating Tumor DNA in Colorectal Cancer

Objective: Circulating tumor DNA (ctDNA) is a candidate biomarker of cancer with practice-changing potential in the detection of both early and residual disease. Disease stage and tumor size affect the probability of ctDNA detection, whereas little is known about the influence of other tumor characteristics on ctDNA detection. This study investigates the impact of tumor cell whole-genome doubling (WGD) on the detection of ctDNA in plasma collected preoperatively from newly diagnosed colorectal cancer (CRC) patients. Methods: WGD was estimated from copy numbers derived from whole-exome sequencing (WES) data of matched tumor and normal DNA from 833 Danish CRC patients. To explore if tumor WGD status impacts ctDNA detection, we applied tumor-informed ctDNA analysis to preoperative plasma samples from all patients. Results: Patients with WGD+ tumors had 53% increased odds of being ctDNA positive (OR = 1.53, 95%CI: 1.12–2.09). After stratification for UICC stage, the association persisted for Stage I (OR = 2.44, 95%CI: 1.22–5.03) and Stage II (OR = 1.76, 95%CI: 1.11–2.81) but not for Stage III (OR = 0.83, 95%CI: 0.44–1.53) patients. Conclusion: The presence of WGD significantly increases the probability of detecting ctDNA, particularly for early-stage disease. In patients with more advanced disease, the benefit of WGD on ctDNA detection is less pronounced, consistent with increased DNA shedding from these tumors, making ctDNA detection less dependent on the amount of ctDNA released per tumor cell

Exchange of nutrients and oxygen across the sediment-water interface below a Sparus aurata marine fish farm in the north-western Mediterranean Sea

Purpose: This study analyzes the effects of aquaculture activities in open seawater in the north-western coastal waters of the Mediterranean Sea. It is the first of its kind to be based on benthic flux data gathered in situ below fish farms for this particular area. Materials and methods: Samples were collected on four sampling campaigns over a 1-year cycle under a Sparus aurata fish farm facility where benthic fluxes were measured in situ using light and dark benthic chambers. Bottom water and sediment samples were also collected. Data were compared to those for a nearby control station. Results and discussion: Significant differences were found (ANOVA, p < 0. 05) between concentrations of organic matter (OM), total phosphorus and redox potentials in sediments located under the cages and those of the control station. The consumption of dissolved oxygen (DO) by sediment and positive ammonium (NH4 +) fluxes was stimulated by OM content, with correlations of r = -0. 60 (p < 0. 01) and r = 0. 70 (p < 0. 01), respectively. The OM content of sediments was found to be consistently higher under the cages than at the control station, with the highest value (1. 8 ± 0. 7 %) under the cages observed during the early summer; values of DO and NH4 + fluxes were -64 ± 17 and 12. 7 ± 1. 0 mmol m-2 day-1, respectively. PO4 3- fluxes were consistently higher in the fish farm sediments (between 0. 58 and 0. 98 mmol m-2 day-1) than those observed at the control station. Nitrate (NO3 -) fluxes were found to be consistently negative due to denitrification occurring in the sediments and were related to the concentration of NO3 - in bottom waters (r = 0. 92, p < 0. 01). Si fluxes were shown to be associated with water temperature (r = 0. 59, p < 0. 05). Conclusions: The results imply that sediments located below cages accumulate organic matter originating from aquaculture activities, especially during summer months when this activity increases. Sediments undergo biogeochemical changes that mainly affect fluxes of DO, NH4 + and soluble reactive phosphorus, although these do not seem to have a significant impact on the quality of the water column due to the hydrodynamic characteristics of the area. © 2012 Springer-Verlag.We would like to thank the Caja del Mediterraneo for a predoctoral fellowship fund for this research and Antonio Asuncion Acuigroup Maremar manager for the facilities and support in conducting the study. The translation of this paper was funded by the Universidad Politecnica de Valencia, Spain. We are grateful for the valuable comments of the anonymous reviewers on previous versions of the manuscript.Morata Higón, T.; Sospedra, J.; Falco Giaccaglia, SL.; Rodilla Alama, M. (2012). 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Benthic fluxes of oxygen and nutrients in sublittoral fine sands in a north-western Mediterranean coastal area

[EN] Traditionally, benthic metabolism in sublittoral permeable sands have not been widely studied, although these sands can have a direct and transcendental impact in coastal ecosystems. This study aims to determine oxygen and nutrient fluxes at the sediment-water interface and the study of possible interactions among environmental variables and the benthic metabolism in well-sorted fine sands. Eight sampling campaigns were carried out over the annual cycle in the eastern coast of Spain (NW Mediterranean) at 9 m depth station with permeable bottoms. Water column and sediment samples were collected in order to determine physico-chemical and biological variables. Moreover, in situ incubations were performed to estimate the exchange of dissolved solutes in the sediment-water interface using dark and light benthic chambers. Biochemical compounds at the sediment surface ranged between 160 and 744 mu g g(-1) for proteins, 296 and 702 mu g g(-1) for carbohydrates, and between 327 and 1224 [mu g C g(-1) for biopolymeric carbon. Chloroplastic pigment equivalents in sediments were mainly composed by chlorophyll a (1.81-2.89 mu g g(-1)). These sedimentary organic descriptors indicated oligotrophic conditions according to the biochemical approach used. In this sense, the most abundant species in the macrobenthic community were sensitive to organic enrichment. In dark conditions, benthic fluxes behaved as a sink of oxygen and a source of nutrients. Oxygen fluxes (between -26,610 and -10,635 mu mol m(-2) d(-1)) were related with labile organic fraction (r= -0.86, p < 0.01 with biopolymeric carbon; r= -0.91, p < 0.01 with chloroplastic pigment equivalents). Daily fluxes of dissolved oxygen, that were obtained by adding light and dark fluxes, were only positive in spring campaigns (6966 mu mol m(-2) d(-1)) owing to the highest incident irradiance levels (r=0.98, p < 0.01) that stimulate microphytobenthic primary production. Microphytobenthos played an important role on benthic metabolism and was the main primary producer in this coastal ecosystem. However, an average annual uptake of 31 mmol m-2 d(-1) of oxygen and a release of DIN and Si(OH)(4) (329 and 68 mmol m(-2) d(-1) respectively) were estimated in these bottoms, which means heterotrophic conditions. (C) 2015 Elsevier Ltd. All rights reserved.We are grateful for the valuable comments of anonymous reviewers on previous version of the manuscript. This research was supported by the Conselleria d'Educacio (Generalitat Valenciana).Sospedra, J.; Falco, S.; Morata, T.; Gadea, I.; Rodilla, M. (2015). Benthic fluxes of oxygen and nutrients in sublittoral fine sands in a north-western Mediterranean coastal area. Continental Shelf Research. 97:32-42. doi:10.1016/j.csr.2015.02.002S32429