Long-Term Epigenetic Impact of Chemotherapy in Breast Cancer Patients Open Access

Zhong, Chaojie (Spring 2018)

Permanent URL: https://etd.library.emory.edu/concern/etds/9z902z89q?locale=en


Breast cancer is one of the most prevalent cancers among females. Chemotherapy remains an efficacious mainline treatment option, although it is found to be highly toxic and contributes to Cancer Related Fatigue (CRF). The mechanism through which chemotherapy may lower quality of life among breast cancer survivors warrants investigation for its implication in healthcare decisions. Previously, DNA methylation in 3 regions proximal to genes ubiquitin specific peptidase 2 (USP2), SMAD3, and vacuole membrane protein 1 (VMP1) have been associated with prior chemotherapy in breast cancer patients. The difference in DNA methylation was also associated with inflammation, which correlated with CRF. The differential DNA methylation persisted 6 months post treatment as did its association with prior chemotherapy and inflammation. We developed a targeted bisulfite sequencing technique to interrogate specific genomic regions and examined whether significant difference in DNA methylation at these previously identified regions remained 12 months post treatment and whether the difference in DNA methylation was still associated with chemotherapy and inflammation in breast cancer patients from the same cohort. We found that DNA methylation levels at the 3 genomic regions trended lower in patients who received chemotherapy than in those who did not 12 months post treatment, and the difference was statistically significant at 1 region in the gene USP2. DNA methylation at the 3 regions in patients who exhibited higher levels of inflammation and CRF also trended lower 12 months post treatment, but there was no statistically significant association between DNA methylation level and inflammation or CRF. Our findings were consistent with lower levels of DNA methylation at the 3 regions associated with prior chemotherapy, but the difference decayed at 6 months post treatment and further at 12 months post treatment. The results indicate that chemotherapy contributes to persistent CRF in breast cancer patients and imprints the epigenome of peripheral blood mononuclear cells at putative regulatory regions.


Table of Contents

Introduction 1

Breast Cancer Overview 2

Breast Cancer Treatment 3

Breast Cancer Survivorship 5

Cancer Related Fatigue (CRF) 6

Epigenetics 7

Epigenetics and Cancer 9

Thesis Objectives 11

Methods 13

Selecting Methods 14

Targeted Bisulfite Sequencing 15

Analysis of Targeted Bisulfite Sequencing 16

Statistical Analysis 18

Results 19

CRF Project Overview 20

Regions of Interest 23

Relationship between methylation level at specific CpG and chemotherapy status 25

Aggregated methylation level of the 3 regions of interest grouped by patient chemotherapy status 27

Relation between methylation level at specific CpG sites and inflammation or CRF 28

Aggregated methylation level of the 3 regions of interest grouped by patient inflammation level and

CRF ranking 30

The temporal changes of methylation levels at different CpG sites 31

Relationship between methylation level at specific CpG sites and cytokine level 33

Methylation differences between chemotherapy vs. non-chemotherapy groups 36

Discussion 37

1. Interpretation 38

1. Comparatively Lower Methylation Level in the Chemotherapy Treated Group Persisted 39 

2. The Relation between Comparatively Lower Methylation Level and Relevant Factors 39

a. Chemotherapy Status 39

b. Inflammation Level and CRF 40

3. Methylation Changes in Individuals over Time 40

2. Limitation 41

3. Future Direction 42

Reference 45

Supplementary Tables 51

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