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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

The percentage of Alu subfamilies in all colorectal cancer cell lines. A shows that the OxPt and SN38-resistant cell lines consistently show higher percentage of the Alu Y subfamily than their parental cell lines. B and C show the percentages of Alu J and Alu S subfamilies in the cell line models, respectively.
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Fig4: The percentage of Alu subfamilies in all colorectal cancer cell lines. A shows that the OxPt and SN38-resistant cell lines consistently show higher percentage of the Alu Y subfamily than their parental cell lines. B and C show the percentages of Alu J and Alu S subfamilies in the cell line models, respectively.

Mentions: To further validate our findings, we compared RRBS reads that can be uniquely mapped to the human repeat sequence between the drug-resistant cell lines and their parental cell lines. We made a linear normalization of the RRBS data across all the cell lines by making the total amount of mapped RRBS reads of each sample equal. Then we extracted the reads annotated as Alu sequence and compared the number of the reads uniquely mapped to Alu sequences between the drug-resistant cell lines and their parental cell lines. In general, all OxPt and SN38-resistant cell lines consistently show higher number of reads from Alu Y subfamilies than that in their parental cell line. There is only one exception. The SN38-resistant HT-29 cell line showed almost equal number of the reads to its parental cell line. We transformed the read number into log2 format to make the distribution of read number fit a normal distribution. Then we performed a paired t-test, and the statistical result showed that the number of Alu Y reads in the drug-resistant cell lines was significantly higher than that in their matched parental cell lines (p-value = 0.0039 for the SN38 resistant cells vs. the parental cells; p-value = 2.13 × 10−12 for the OxPt resistant cells vs. the parental cells, respectively). Moreover, we calculated the percentage of the reads of Alu subfamily members (Alu Y, Alu J and Alu S) for all the cell line samples. The percentage of the Alu Y subfamily in the OxPt and SN38-resistant cell lines was higher than that in the parental cell lines (Figure 4A). The percentages of Alu J and Alu S subfamilies in all cell lines are shown in Figure 4B and Figure 4C, respectively.Figure 4


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)

The percentage of Alu subfamilies in all colorectal cancer cell lines. A shows that the OxPt and SN38-resistant cell lines consistently show higher percentage of the Alu Y subfamily than their parental cell lines. B and C show the percentages of Alu J and Alu S subfamilies in the cell line models, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: The percentage of Alu subfamilies in all colorectal cancer cell lines. A shows that the OxPt and SN38-resistant cell lines consistently show higher percentage of the Alu Y subfamily than their parental cell lines. B and C show the percentages of Alu J and Alu S subfamilies in the cell line models, respectively.
Mentions: To further validate our findings, we compared RRBS reads that can be uniquely mapped to the human repeat sequence between the drug-resistant cell lines and their parental cell lines. We made a linear normalization of the RRBS data across all the cell lines by making the total amount of mapped RRBS reads of each sample equal. Then we extracted the reads annotated as Alu sequence and compared the number of the reads uniquely mapped to Alu sequences between the drug-resistant cell lines and their parental cell lines. In general, all OxPt and SN38-resistant cell lines consistently show higher number of reads from Alu Y subfamilies than that in their parental cell line. There is only one exception. The SN38-resistant HT-29 cell line showed almost equal number of the reads to its parental cell line. We transformed the read number into log2 format to make the distribution of read number fit a normal distribution. Then we performed a paired t-test, and the statistical result showed that the number of Alu Y reads in the drug-resistant cell lines was significantly higher than that in their matched parental cell lines (p-value = 0.0039 for the SN38 resistant cells vs. the parental cells; p-value = 2.13 × 10−12 for the OxPt resistant cells vs. the parental cells, respectively). Moreover, we calculated the percentage of the reads of Alu subfamily members (Alu Y, Alu J and Alu S) for all the cell line samples. The percentage of the Alu Y subfamily in the OxPt and SN38-resistant cell lines was higher than that in the parental cell lines (Figure 4A). The percentages of Alu J and Alu S subfamilies in all cell lines are shown in Figure 4B and Figure 4C, respectively.Figure 4

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