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

Lin X, Stenvang J, Rasmussen MH, Zhu S, Jensen NF, Tarpgaard LS, Yang G, Belling K, Andersen CL, Li J, Bolund L, Brünner N - BMC Genomics (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedicine, University of Aarhus, the Bartholin Building, DK-8000, Aarhus C, Denmark. xue.lin@biomed.au.dk.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

A shows the percentage of loci overlapping with the simulation in sets A, P, O and S. B shows the percentage of Alu elements, and Alu subfamilies in sets P, O and S, which are not overlapping with the simulation.
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Fig3: A shows the percentage of loci overlapping with the simulation in sets A, P, O and S. B shows the percentage of Alu elements, and Alu subfamilies in sets P, O and S, which are not overlapping with the simulation.

Mentions: Subsequently, we compared the identified loci in the sets P, O and S with the loci in the RRBS simulation (selection section window size is 40-300 bp), respectively. We found that 54.7%, 42.4% and 42.1% loci in the sets P, O and S overlapped with the loci in the simulation (Figure 3A). Moreover, we identified the common loci shared by all nine colorectal cancer cell lines and defined a new set A. When we compared the loci in the set A, we found that 87.7% of the loci in set A overlapped with the loci in the simulation (Figure 3A). A small portion of the overlapping loci reflects the difference of the genomes of the nine cell lines from the human genome reference used in the simulation. This difference might reflect that the colorectal cancer cell lines harbour a certain number of genomic aberrations and these genomic aberrations could lead to some of the difference between the sequenced genomic loci and the loci in the simulation. Notably, set P from the three parental cell lines showed a lower proportion of overlapping loci with the simulation compared with set A, suggesting set P contained more loci related to genomic aberrations in individual cell lines than set A. Interestingly, set P showed higher portion of overlapping loci with the simulation than sets O or S, suggesting that the genomes of OxPt-resistant and SN38-resistant cell lines had larger extents of difference from the human genome reference than the genomes of their parental cell lines. This implies that changes in genomic structure in drug-resistant cell lines might occur during drug treatment. We further analysed the constitution of the non-overlapping loci in sets P, O and S. As in the previous analyses, a considerable amount of Alu elements contributed to the proportion of the non-overlapping loci in sets P, O and S. More impressively, the percentages of Alu elements in sets O and S were increased compared with that in set P. Among Alu subfamily members, we further confirmed that the Alu Y subfamily mainly contributed to the increased proportion of Alu elements in the total non-overlapping loci in the drug-resistant cell lines (Figure 3B). Thus, based on our observation and analysis, we found a correlation between the drug-resistant phenotypes and the increment of Alu Y elements.Figure 3


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

Lin X, Stenvang J, Rasmussen MH, Zhu S, Jensen NF, Tarpgaard LS, Yang G, Belling K, Andersen CL, Li J, Bolund L, Brünner N - BMC Genomics (2015)

A shows the percentage of loci overlapping with the simulation in sets A, P, O and S. B shows the percentage of Alu elements, and Alu subfamilies in sets P, O and S, which are not overlapping with the simulation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4440512&req=5

Fig3: A shows the percentage of loci overlapping with the simulation in sets A, P, O and S. B shows the percentage of Alu elements, and Alu subfamilies in sets P, O and S, which are not overlapping with the simulation.
Mentions: Subsequently, we compared the identified loci in the sets P, O and S with the loci in the RRBS simulation (selection section window size is 40-300 bp), respectively. We found that 54.7%, 42.4% and 42.1% loci in the sets P, O and S overlapped with the loci in the simulation (Figure 3A). Moreover, we identified the common loci shared by all nine colorectal cancer cell lines and defined a new set A. When we compared the loci in the set A, we found that 87.7% of the loci in set A overlapped with the loci in the simulation (Figure 3A). A small portion of the overlapping loci reflects the difference of the genomes of the nine cell lines from the human genome reference used in the simulation. This difference might reflect that the colorectal cancer cell lines harbour a certain number of genomic aberrations and these genomic aberrations could lead to some of the difference between the sequenced genomic loci and the loci in the simulation. Notably, set P from the three parental cell lines showed a lower proportion of overlapping loci with the simulation compared with set A, suggesting set P contained more loci related to genomic aberrations in individual cell lines than set A. Interestingly, set P showed higher portion of overlapping loci with the simulation than sets O or S, suggesting that the genomes of OxPt-resistant and SN38-resistant cell lines had larger extents of difference from the human genome reference than the genomes of their parental cell lines. This implies that changes in genomic structure in drug-resistant cell lines might occur during drug treatment. We further analysed the constitution of the non-overlapping loci in sets P, O and S. As in the previous analyses, a considerable amount of Alu elements contributed to the proportion of the non-overlapping loci in sets P, O and S. More impressively, the percentages of Alu elements in sets O and S were increased compared with that in set P. Among Alu subfamily members, we further confirmed that the Alu Y subfamily mainly contributed to the increased proportion of Alu elements in the total non-overlapping loci in the drug-resistant cell lines (Figure 3B). Thus, based on our observation and analysis, we found a correlation between the drug-resistant phenotypes and the increment of Alu Y elements.Figure 3

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedicine, University of Aarhus, the Bartholin Building, DK-8000, Aarhus C, Denmark. xue.lin@biomed.au.dk.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus