Genomic and epigenomic integration identifies a prognostic signature in colon cancer

Joo Mi Yi, Mashaal Dhir, Leander Van Neste, Stephanie R. Downing, Jana Jeschke, Sabine C. Glockner, Marilia De Freitas Calmon, Craig M. Hooker, Juan M. Funes, Chris Boshoff, Kim M. Smits, Manon Van Engeland, Matty P. Weijenberg, Christine A. Iacobuzio-Donahue, James G. Herman, Kornel Schuebel, Stephen B Baylin, Nita Ahuja

Research output: Contribution to journalArticle

Abstract

Purpose: The importance of genetic and epigenetic alterations maybe in their aggregate role in altering core pathways in tumorigenesis. Experimental Design: Merging genome-wide genomic and epigenomic alterations, we identify key genes and pathways altered in colorectal cancers (CRC). DNA methylation analysis was tested for predicting survival in CRC patients using Cox proportional hazard model. Results: We identified 29 low frequency-mutated genes that are also inactivated by epigenetic mechanisms in CRC. Pathway analysis showed the extracellular matrix (ECM) remodeling pathway is silenced in CRC. Six ECM pathway genes were tested for their prognostic potential in large CRC cohorts (n = 777). DNA methylation of IGFBP3 and EVL predicted for poor survival (IGFBP3: HR = 2.58, 95% CI: 1.37-4.87, P = 0.004; EVL: HR = 2.48, 95% CI: 1.07-5.74, P = 0.034) and simultaneous methylation of multiple genes predicted significantly worse survival (HR = 8.61, 95% CI: 2.16-34.36, P <0.001 for methylation of IGFBP3, EVL, CD109, and FLNC). DNA methylation of IGFBP3 and EVL was validated as a prognostic marker in an independent contemporary-matched cohort (IGFBP3 HR = 2.06, 95% CI: 1.04-4.09, P = 0.038; EVL HR = 2.23, 95% CI: 1.00-5.0, P = 0.05) and EVL DNA methylation remained significant in a secondary historical validation cohort (HR = 1.41, 95% CI: 1.05-1.89, P = 0.022). Moreover, DNA methylation of selected ECM genes helps to stratify the high-risk stage 2 colon cancers patients who would benefit from adjuvant chemotherapy (HR: 5.85, 95% CI: 2.03-16.83, P = 0.001 for simultaneous methylation of IGFBP3, EVL, and CD109). Conclusions: CRC that have silenced genes in ECM pathway components show worse survival suggesting that our finding provides novel prognostic biomarkers for CRC and reflects the high importance of integrative analyses linking genetic and epigenetic abnormalities with pathway disruption in cancer.

Original languageEnglish (US)
Pages (from-to)1535-1545
Number of pages11
JournalClinical Cancer Research
Volume17
Issue number6
DOIs
StatePublished - Mar 15 2011

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Epigenomics
Colonic Neoplasms
Colorectal Neoplasms
DNA Methylation
Extracellular Matrix
Methylation
Survival
Genes
Adjuvant Chemotherapy
Proportional Hazards Models
Gene Frequency
Carcinogenesis
Research Design
Biomarkers
Genome
Neoplasms

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

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Genomic and epigenomic integration identifies a prognostic signature in colon cancer. / Yi, Joo Mi; Dhir, Mashaal; Van Neste, Leander; Downing, Stephanie R.; Jeschke, Jana; Glockner, Sabine C.; Calmon, Marilia De Freitas; Hooker, Craig M.; Funes, Juan M.; Boshoff, Chris; Smits, Kim M.; Van Engeland, Manon; Weijenberg, Matty P.; Iacobuzio-Donahue, Christine A.; Herman, James G.; Schuebel, Kornel; Baylin, Stephen B; Ahuja, Nita.

In: Clinical Cancer Research, Vol. 17, No. 6, 15.03.2011, p. 1535-1545.

Research output: Contribution to journalArticle

Yi, JM, Dhir, M, Van Neste, L, Downing, SR, Jeschke, J, Glockner, SC, Calmon, MDF, Hooker, CM, Funes, JM, Boshoff, C, Smits, KM, Van Engeland, M, Weijenberg, MP, Iacobuzio-Donahue, CA, Herman, JG, Schuebel, K, Baylin, SB & Ahuja, N 2011, 'Genomic and epigenomic integration identifies a prognostic signature in colon cancer', Clinical Cancer Research, vol. 17, no. 6, pp. 1535-1545. https://doi.org/10.1158/1078-0432.CCR-10-2509
Yi JM, Dhir M, Van Neste L, Downing SR, Jeschke J, Glockner SC et al. Genomic and epigenomic integration identifies a prognostic signature in colon cancer. Clinical Cancer Research. 2011 Mar 15;17(6):1535-1545. https://doi.org/10.1158/1078-0432.CCR-10-2509
Yi, Joo Mi ; Dhir, Mashaal ; Van Neste, Leander ; Downing, Stephanie R. ; Jeschke, Jana ; Glockner, Sabine C. ; Calmon, Marilia De Freitas ; Hooker, Craig M. ; Funes, Juan M. ; Boshoff, Chris ; Smits, Kim M. ; Van Engeland, Manon ; Weijenberg, Matty P. ; Iacobuzio-Donahue, Christine A. ; Herman, James G. ; Schuebel, Kornel ; Baylin, Stephen B ; Ahuja, Nita. / Genomic and epigenomic integration identifies a prognostic signature in colon cancer. In: Clinical Cancer Research. 2011 ; Vol. 17, No. 6. pp. 1535-1545.
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abstract = "Purpose: The importance of genetic and epigenetic alterations maybe in their aggregate role in altering core pathways in tumorigenesis. Experimental Design: Merging genome-wide genomic and epigenomic alterations, we identify key genes and pathways altered in colorectal cancers (CRC). DNA methylation analysis was tested for predicting survival in CRC patients using Cox proportional hazard model. Results: We identified 29 low frequency-mutated genes that are also inactivated by epigenetic mechanisms in CRC. Pathway analysis showed the extracellular matrix (ECM) remodeling pathway is silenced in CRC. Six ECM pathway genes were tested for their prognostic potential in large CRC cohorts (n = 777). DNA methylation of IGFBP3 and EVL predicted for poor survival (IGFBP3: HR = 2.58, 95{\%} CI: 1.37-4.87, P = 0.004; EVL: HR = 2.48, 95{\%} CI: 1.07-5.74, P = 0.034) and simultaneous methylation of multiple genes predicted significantly worse survival (HR = 8.61, 95{\%} CI: 2.16-34.36, P <0.001 for methylation of IGFBP3, EVL, CD109, and FLNC). DNA methylation of IGFBP3 and EVL was validated as a prognostic marker in an independent contemporary-matched cohort (IGFBP3 HR = 2.06, 95{\%} CI: 1.04-4.09, P = 0.038; EVL HR = 2.23, 95{\%} CI: 1.00-5.0, P = 0.05) and EVL DNA methylation remained significant in a secondary historical validation cohort (HR = 1.41, 95{\%} CI: 1.05-1.89, P = 0.022). Moreover, DNA methylation of selected ECM genes helps to stratify the high-risk stage 2 colon cancers patients who would benefit from adjuvant chemotherapy (HR: 5.85, 95{\%} CI: 2.03-16.83, P = 0.001 for simultaneous methylation of IGFBP3, EVL, and CD109). Conclusions: CRC that have silenced genes in ECM pathway components show worse survival suggesting that our finding provides novel prognostic biomarkers for CRC and reflects the high importance of integrative analyses linking genetic and epigenetic abnormalities with pathway disruption in cancer.",
author = "Yi, {Joo Mi} and Mashaal Dhir and {Van Neste}, Leander and Downing, {Stephanie R.} and Jana Jeschke and Glockner, {Sabine C.} and Calmon, {Marilia De Freitas} and Hooker, {Craig M.} and Funes, {Juan M.} and Chris Boshoff and Smits, {Kim M.} and {Van Engeland}, Manon and Weijenberg, {Matty P.} and Iacobuzio-Donahue, {Christine A.} and Herman, {James G.} and Kornel Schuebel and Baylin, {Stephen B} and Nita Ahuja",
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T1 - Genomic and epigenomic integration identifies a prognostic signature in colon cancer

AU - Yi, Joo Mi

AU - Dhir, Mashaal

AU - Van Neste, Leander

AU - Downing, Stephanie R.

AU - Jeschke, Jana

AU - Glockner, Sabine C.

AU - Calmon, Marilia De Freitas

AU - Hooker, Craig M.

AU - Funes, Juan M.

AU - Boshoff, Chris

AU - Smits, Kim M.

AU - Van Engeland, Manon

AU - Weijenberg, Matty P.

AU - Iacobuzio-Donahue, Christine A.

AU - Herman, James G.

AU - Schuebel, Kornel

AU - Baylin, Stephen B

AU - Ahuja, Nita

PY - 2011/3/15

Y1 - 2011/3/15

N2 - Purpose: The importance of genetic and epigenetic alterations maybe in their aggregate role in altering core pathways in tumorigenesis. Experimental Design: Merging genome-wide genomic and epigenomic alterations, we identify key genes and pathways altered in colorectal cancers (CRC). DNA methylation analysis was tested for predicting survival in CRC patients using Cox proportional hazard model. Results: We identified 29 low frequency-mutated genes that are also inactivated by epigenetic mechanisms in CRC. Pathway analysis showed the extracellular matrix (ECM) remodeling pathway is silenced in CRC. Six ECM pathway genes were tested for their prognostic potential in large CRC cohorts (n = 777). DNA methylation of IGFBP3 and EVL predicted for poor survival (IGFBP3: HR = 2.58, 95% CI: 1.37-4.87, P = 0.004; EVL: HR = 2.48, 95% CI: 1.07-5.74, P = 0.034) and simultaneous methylation of multiple genes predicted significantly worse survival (HR = 8.61, 95% CI: 2.16-34.36, P <0.001 for methylation of IGFBP3, EVL, CD109, and FLNC). DNA methylation of IGFBP3 and EVL was validated as a prognostic marker in an independent contemporary-matched cohort (IGFBP3 HR = 2.06, 95% CI: 1.04-4.09, P = 0.038; EVL HR = 2.23, 95% CI: 1.00-5.0, P = 0.05) and EVL DNA methylation remained significant in a secondary historical validation cohort (HR = 1.41, 95% CI: 1.05-1.89, P = 0.022). Moreover, DNA methylation of selected ECM genes helps to stratify the high-risk stage 2 colon cancers patients who would benefit from adjuvant chemotherapy (HR: 5.85, 95% CI: 2.03-16.83, P = 0.001 for simultaneous methylation of IGFBP3, EVL, and CD109). Conclusions: CRC that have silenced genes in ECM pathway components show worse survival suggesting that our finding provides novel prognostic biomarkers for CRC and reflects the high importance of integrative analyses linking genetic and epigenetic abnormalities with pathway disruption in cancer.

AB - Purpose: The importance of genetic and epigenetic alterations maybe in their aggregate role in altering core pathways in tumorigenesis. Experimental Design: Merging genome-wide genomic and epigenomic alterations, we identify key genes and pathways altered in colorectal cancers (CRC). DNA methylation analysis was tested for predicting survival in CRC patients using Cox proportional hazard model. Results: We identified 29 low frequency-mutated genes that are also inactivated by epigenetic mechanisms in CRC. Pathway analysis showed the extracellular matrix (ECM) remodeling pathway is silenced in CRC. Six ECM pathway genes were tested for their prognostic potential in large CRC cohorts (n = 777). DNA methylation of IGFBP3 and EVL predicted for poor survival (IGFBP3: HR = 2.58, 95% CI: 1.37-4.87, P = 0.004; EVL: HR = 2.48, 95% CI: 1.07-5.74, P = 0.034) and simultaneous methylation of multiple genes predicted significantly worse survival (HR = 8.61, 95% CI: 2.16-34.36, P <0.001 for methylation of IGFBP3, EVL, CD109, and FLNC). DNA methylation of IGFBP3 and EVL was validated as a prognostic marker in an independent contemporary-matched cohort (IGFBP3 HR = 2.06, 95% CI: 1.04-4.09, P = 0.038; EVL HR = 2.23, 95% CI: 1.00-5.0, P = 0.05) and EVL DNA methylation remained significant in a secondary historical validation cohort (HR = 1.41, 95% CI: 1.05-1.89, P = 0.022). Moreover, DNA methylation of selected ECM genes helps to stratify the high-risk stage 2 colon cancers patients who would benefit from adjuvant chemotherapy (HR: 5.85, 95% CI: 2.03-16.83, P = 0.001 for simultaneous methylation of IGFBP3, EVL, and CD109). Conclusions: CRC that have silenced genes in ECM pathway components show worse survival suggesting that our finding provides novel prognostic biomarkers for CRC and reflects the high importance of integrative analyses linking genetic and epigenetic abnormalities with pathway disruption in cancer.

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