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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

Alu Y subfamily enrichment. A: the number of selected loci in the sets P, O and S (see text). B: the percentage of the Alu Y subfamily out of the identified Alu elements in set E. C: the percentage of Alu elements in all cytosine loci and the percentage of the Alu Y subfamily in the identified Alu elements in either sliding windows of fixed size or extended size in RRBS in-silico simulation.
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Fig2: Alu Y subfamily enrichment. A: the number of selected loci in the sets P, O and S (see text). B: the percentage of the Alu Y subfamily out of the identified Alu elements in set E. C: the percentage of Alu elements in all cytosine loci and the percentage of the Alu Y subfamily in the identified Alu elements in either sliding windows of fixed size or extended size in RRBS in-silico simulation.

Mentions: By analysing RRBS data for the colorectal cancer cell line models, we identified the loci unique to the three parental cell lines (cell line A (HCT-116 parental), D (HT-29 parental) and G (LoVo parental)) and defined a set P, which contains only these parental cell line loci (including the three formats of CpG, CHG and CHH). We then identified loci unique to the three OxPt-resistant sub-lines (cell line B (HCT-116 OxPt resistant), E (HT-29 OxPt resistant) and H (LoVo OxPt resistant)) as uniquely representing OxPt-resistant DNA methylation features and defined a set O, which contains only these OxPt-resistant sub-line loci (including the three formats of CpG, CHG and CHH). Finally, we identified the loci unique to the three SN38-resistant sub-lines (cell line C (HCT-116 SN38 resistant), F (HT-29 SN38 resistant) and I (LoVo SN38 resistant)) as uniquely representing SN38-resistant DNA methylation features and defined a set S, which contains only these SN38-resistant sub-line loci (including the three formats of CpG, CHG and CHH). The numbers of the identified loci in sets P, O and S are shown in Figure 2A. The definitions of the different sets in this study are available in the Additional file 3: Table S2. Taking the identified loci in the context of CpG as an example, there were 505,147, 337,242 and 359,770 cytosine loci identified as uniquely representing drug-sensitive DNA methylation features in the parental (P), OxPt-resistant (O), and SN38-resistant (S) cell-lines respectively.Figure 2


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)

Alu Y subfamily enrichment. A: the number of selected loci in the sets P, O and S (see text). B: the percentage of the Alu Y subfamily out of the identified Alu elements in set E. C: the percentage of Alu elements in all cytosine loci and the percentage of the Alu Y subfamily in the identified Alu elements in either sliding windows of fixed size or extended size in RRBS in-silico simulation.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Alu Y subfamily enrichment. A: the number of selected loci in the sets P, O and S (see text). B: the percentage of the Alu Y subfamily out of the identified Alu elements in set E. C: the percentage of Alu elements in all cytosine loci and the percentage of the Alu Y subfamily in the identified Alu elements in either sliding windows of fixed size or extended size in RRBS in-silico simulation.
Mentions: By analysing RRBS data for the colorectal cancer cell line models, we identified the loci unique to the three parental cell lines (cell line A (HCT-116 parental), D (HT-29 parental) and G (LoVo parental)) and defined a set P, which contains only these parental cell line loci (including the three formats of CpG, CHG and CHH). We then identified loci unique to the three OxPt-resistant sub-lines (cell line B (HCT-116 OxPt resistant), E (HT-29 OxPt resistant) and H (LoVo OxPt resistant)) as uniquely representing OxPt-resistant DNA methylation features and defined a set O, which contains only these OxPt-resistant sub-line loci (including the three formats of CpG, CHG and CHH). Finally, we identified the loci unique to the three SN38-resistant sub-lines (cell line C (HCT-116 SN38 resistant), F (HT-29 SN38 resistant) and I (LoVo SN38 resistant)) as uniquely representing SN38-resistant DNA methylation features and defined a set S, which contains only these SN38-resistant sub-line loci (including the three formats of CpG, CHG and CHH). The numbers of the identified loci in sets P, O and S are shown in Figure 2A. The definitions of the different sets in this study are available in the Additional file 3: Table S2. Taking the identified loci in the context of CpG as an example, there were 505,147, 337,242 and 359,770 cytosine loci identified as uniquely representing drug-sensitive DNA methylation features in the parental (P), OxPt-resistant (O), and SN38-resistant (S) cell-lines respectively.Figure 2

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