Tumor hypomethylation at 6p21.3 associates with longer time to recurrence of high-grade serous epithelial ovarian cancer

Chen Wang, Mine S. Cicek, Bridget Charbonneau, Kimberly R. Kalli, Sebastian M. Armasu, Melissa C. Larson, Gottfried E. Konecny, Boris Winterhoff, Jian Bing Fan, Marina Bibikova, Jeremy Chien, Viji Shridhar, Matthew S. Block, Lynn C. Hartmann, Daniel W. Visscher, Julie M. Cunningham, Keith L. Knutson, Brooke L. Fridley, Ellen L. Goode

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

To reveal biologic mechanisms underlying clinical outcome of high-grade serous (HGS) epithelial ovarian carcinomas (EOC), we evaluated the association between tumor epigenetic changes and time to recurrence (TTR). We assessed methylation at approximately 450,000 genome-wide CpGs in tumors of 337 Mayo Clinic (Rochester, MN) patients. Semi-supervised clustering of discovery (n = 168) and validation (n = 169) sets was used to determine clinically relevant methylation classes. Clustering identified two methylation classes based on 60 informative CpGs, which differed in TTR in the validation set [R vs. L class, P = 2.9 × 10-3, HR = 0.52; 95% confidence interval (CI), 0.34-0.80]. Follow-up analyses considered genome-wide tumor mRNA expression (n = 104) and CD8 T-cell infiltration (n = 89) in patient subsets. Hypomethylation of CpGs located in 6p21.3 in the R class associated with cis upregulation of genes enriched in immune response processes (TAP1, PSMB8, PSMB9, HLA-DQB1, HLA-DQB2, HLA-DMA, and HLA-DOA), increased CD8 T-cell tumor infiltration (P = 7.6 × 10-5), and trans-regulation of genes in immune-related pathways (P = 1.6 × 10-32). This is the most comprehensive assessment of clinical outcomes with regard to epithelial ovarian carcinoma tumor methylation to date. Collectively, these results suggest that an epigenetically mediated immune response is a predictor of recurrence and, possibly, treatment response for HGS EOC.

Original languageEnglish (US)
Pages (from-to)3084-3091
Number of pages8
JournalCancer Research
Volume74
Issue number11
DOIs
StatePublished - Jun 1 2014
Externally publishedYes

Fingerprint

Methylation
Recurrence
Neoplasms
Carcinoma
Cluster Analysis
Genome
T-Lymphocytes
Epigenomics
Genes
Up-Regulation
Outcome Assessment (Health Care)
Ovarian epithelial cancer
Confidence Intervals
Messenger RNA
Therapeutics

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Wang, C., Cicek, M. S., Charbonneau, B., Kalli, K. R., Armasu, S. M., Larson, M. C., ... Goode, E. L. (2014). Tumor hypomethylation at 6p21.3 associates with longer time to recurrence of high-grade serous epithelial ovarian cancer. Cancer Research, 74(11), 3084-3091. https://doi.org/10.1158/0008-5472.CAN-13-3198

Tumor hypomethylation at 6p21.3 associates with longer time to recurrence of high-grade serous epithelial ovarian cancer. / Wang, Chen; Cicek, Mine S.; Charbonneau, Bridget; Kalli, Kimberly R.; Armasu, Sebastian M.; Larson, Melissa C.; Konecny, Gottfried E.; Winterhoff, Boris; Fan, Jian Bing; Bibikova, Marina; Chien, Jeremy; Shridhar, Viji; Block, Matthew S.; Hartmann, Lynn C.; Visscher, Daniel W.; Cunningham, Julie M.; Knutson, Keith L.; Fridley, Brooke L.; Goode, Ellen L.

In: Cancer Research, Vol. 74, No. 11, 01.06.2014, p. 3084-3091.

Research output: Contribution to journalArticle

Wang, C, Cicek, MS, Charbonneau, B, Kalli, KR, Armasu, SM, Larson, MC, Konecny, GE, Winterhoff, B, Fan, JB, Bibikova, M, Chien, J, Shridhar, V, Block, MS, Hartmann, LC, Visscher, DW, Cunningham, JM, Knutson, KL, Fridley, BL & Goode, EL 2014, 'Tumor hypomethylation at 6p21.3 associates with longer time to recurrence of high-grade serous epithelial ovarian cancer', Cancer Research, vol. 74, no. 11, pp. 3084-3091. https://doi.org/10.1158/0008-5472.CAN-13-3198
Wang, Chen ; Cicek, Mine S. ; Charbonneau, Bridget ; Kalli, Kimberly R. ; Armasu, Sebastian M. ; Larson, Melissa C. ; Konecny, Gottfried E. ; Winterhoff, Boris ; Fan, Jian Bing ; Bibikova, Marina ; Chien, Jeremy ; Shridhar, Viji ; Block, Matthew S. ; Hartmann, Lynn C. ; Visscher, Daniel W. ; Cunningham, Julie M. ; Knutson, Keith L. ; Fridley, Brooke L. ; Goode, Ellen L. / Tumor hypomethylation at 6p21.3 associates with longer time to recurrence of high-grade serous epithelial ovarian cancer. In: Cancer Research. 2014 ; Vol. 74, No. 11. pp. 3084-3091.
@article{4d280aff8e2c4a5199f04458a1ee6138,
title = "Tumor hypomethylation at 6p21.3 associates with longer time to recurrence of high-grade serous epithelial ovarian cancer",
abstract = "To reveal biologic mechanisms underlying clinical outcome of high-grade serous (HGS) epithelial ovarian carcinomas (EOC), we evaluated the association between tumor epigenetic changes and time to recurrence (TTR). We assessed methylation at approximately 450,000 genome-wide CpGs in tumors of 337 Mayo Clinic (Rochester, MN) patients. Semi-supervised clustering of discovery (n = 168) and validation (n = 169) sets was used to determine clinically relevant methylation classes. Clustering identified two methylation classes based on 60 informative CpGs, which differed in TTR in the validation set [R vs. L class, P = 2.9 × 10-3, HR = 0.52; 95{\%} confidence interval (CI), 0.34-0.80]. Follow-up analyses considered genome-wide tumor mRNA expression (n = 104) and CD8 T-cell infiltration (n = 89) in patient subsets. Hypomethylation of CpGs located in 6p21.3 in the R class associated with cis upregulation of genes enriched in immune response processes (TAP1, PSMB8, PSMB9, HLA-DQB1, HLA-DQB2, HLA-DMA, and HLA-DOA), increased CD8 T-cell tumor infiltration (P = 7.6 × 10-5), and trans-regulation of genes in immune-related pathways (P = 1.6 × 10-32). This is the most comprehensive assessment of clinical outcomes with regard to epithelial ovarian carcinoma tumor methylation to date. Collectively, these results suggest that an epigenetically mediated immune response is a predictor of recurrence and, possibly, treatment response for HGS EOC.",
author = "Chen Wang and Cicek, {Mine S.} and Bridget Charbonneau and Kalli, {Kimberly R.} and Armasu, {Sebastian M.} and Larson, {Melissa C.} and Konecny, {Gottfried E.} and Boris Winterhoff and Fan, {Jian Bing} and Marina Bibikova and Jeremy Chien and Viji Shridhar and Block, {Matthew S.} and Hartmann, {Lynn C.} and Visscher, {Daniel W.} and Cunningham, {Julie M.} and Knutson, {Keith L.} and Fridley, {Brooke L.} and Goode, {Ellen L.}",
year = "2014",
month = "6",
day = "1",
doi = "10.1158/0008-5472.CAN-13-3198",
language = "English (US)",
volume = "74",
pages = "3084--3091",
journal = "Cancer Research",
issn = "0008-5472",
number = "11",

}

TY - JOUR

T1 - Tumor hypomethylation at 6p21.3 associates with longer time to recurrence of high-grade serous epithelial ovarian cancer

AU - Wang, Chen

AU - Cicek, Mine S.

AU - Charbonneau, Bridget

AU - Kalli, Kimberly R.

AU - Armasu, Sebastian M.

AU - Larson, Melissa C.

AU - Konecny, Gottfried E.

AU - Winterhoff, Boris

AU - Fan, Jian Bing

AU - Bibikova, Marina

AU - Chien, Jeremy

AU - Shridhar, Viji

AU - Block, Matthew S.

AU - Hartmann, Lynn C.

AU - Visscher, Daniel W.

AU - Cunningham, Julie M.

AU - Knutson, Keith L.

AU - Fridley, Brooke L.

AU - Goode, Ellen L.

PY - 2014/6/1

Y1 - 2014/6/1

N2 - To reveal biologic mechanisms underlying clinical outcome of high-grade serous (HGS) epithelial ovarian carcinomas (EOC), we evaluated the association between tumor epigenetic changes and time to recurrence (TTR). We assessed methylation at approximately 450,000 genome-wide CpGs in tumors of 337 Mayo Clinic (Rochester, MN) patients. Semi-supervised clustering of discovery (n = 168) and validation (n = 169) sets was used to determine clinically relevant methylation classes. Clustering identified two methylation classes based on 60 informative CpGs, which differed in TTR in the validation set [R vs. L class, P = 2.9 × 10-3, HR = 0.52; 95% confidence interval (CI), 0.34-0.80]. Follow-up analyses considered genome-wide tumor mRNA expression (n = 104) and CD8 T-cell infiltration (n = 89) in patient subsets. Hypomethylation of CpGs located in 6p21.3 in the R class associated with cis upregulation of genes enriched in immune response processes (TAP1, PSMB8, PSMB9, HLA-DQB1, HLA-DQB2, HLA-DMA, and HLA-DOA), increased CD8 T-cell tumor infiltration (P = 7.6 × 10-5), and trans-regulation of genes in immune-related pathways (P = 1.6 × 10-32). This is the most comprehensive assessment of clinical outcomes with regard to epithelial ovarian carcinoma tumor methylation to date. Collectively, these results suggest that an epigenetically mediated immune response is a predictor of recurrence and, possibly, treatment response for HGS EOC.

AB - To reveal biologic mechanisms underlying clinical outcome of high-grade serous (HGS) epithelial ovarian carcinomas (EOC), we evaluated the association between tumor epigenetic changes and time to recurrence (TTR). We assessed methylation at approximately 450,000 genome-wide CpGs in tumors of 337 Mayo Clinic (Rochester, MN) patients. Semi-supervised clustering of discovery (n = 168) and validation (n = 169) sets was used to determine clinically relevant methylation classes. Clustering identified two methylation classes based on 60 informative CpGs, which differed in TTR in the validation set [R vs. L class, P = 2.9 × 10-3, HR = 0.52; 95% confidence interval (CI), 0.34-0.80]. Follow-up analyses considered genome-wide tumor mRNA expression (n = 104) and CD8 T-cell infiltration (n = 89) in patient subsets. Hypomethylation of CpGs located in 6p21.3 in the R class associated with cis upregulation of genes enriched in immune response processes (TAP1, PSMB8, PSMB9, HLA-DQB1, HLA-DQB2, HLA-DMA, and HLA-DOA), increased CD8 T-cell tumor infiltration (P = 7.6 × 10-5), and trans-regulation of genes in immune-related pathways (P = 1.6 × 10-32). This is the most comprehensive assessment of clinical outcomes with regard to epithelial ovarian carcinoma tumor methylation to date. Collectively, these results suggest that an epigenetically mediated immune response is a predictor of recurrence and, possibly, treatment response for HGS EOC.

UR - http://www.scopus.com/inward/record.url?scp=84902133505&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84902133505&partnerID=8YFLogxK

U2 - 10.1158/0008-5472.CAN-13-3198

DO - 10.1158/0008-5472.CAN-13-3198

M3 - Article

C2 - 24728075

AN - SCOPUS:84902133505

VL - 74

SP - 3084

EP - 3091

JO - Cancer Research

JF - Cancer Research

SN - 0008-5472

IS - 11

ER -