Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes

Frank A Sinicrope, Qian D Shi, Thomas Christopher Smyrk, Stephen N Thibodeau, Rodrigo Dienstmann, Justin Guinney, Brian M. Bot, Sabine Tejpar, Mauro Delorenzi, Richard M. Goldberg, Michelle Mahoney, Daniel J. Sargent, Steven Robert Alberts

Research output: Contribution to journalArticle

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Abstract

BACKGROUND & AIMS: Categorization of colon cancers into distinct subtypes using a combination of pathway-based biomarkers could provide insight into stage-independent variability in outcomes. METHODS: We used a polymerase chain reaction-based assay to detect mutations in BRAF (V600E) and in KRAS in 2720 stage III cancer samples, collected prospectively from patients participating in an adjuvant chemotherapy trial (NCCTG N0147). Tumors deficient or proficient in DNA mismatch repair (MMR) were identified based on detection of MLH1, MSH2, and MSH6 proteins and methylation of the MLH1 promoter. Findings were validated using tumor samples from a separate set of patients with stage III cancer (n = 783). Association with 5-year disease-free survival was evaluated using Cox proportional hazards models. RESULTS: Tumors were categorized into 5 subtypes based on MMR status and detection of BRAF or KRAS mutations which were mutually exclusive. Three subtypes were MMR proficient: those with mutations in BRAF (6.9% of samples), mutations in KRAS (35%), or tumors lacking either BRAF or KRAS mutations (49%). Two subtypes were MMR deficient: the sporadic type (6.8%) with BRAF mutation and/or or hypermethylation of MLH1 and the familial type (2.6%), which lacked BRAFV600E or hypermethylation of MLH1. A higher percentage of MMR-proficient tumors with BRAFV600E were proximal (76%), high-grade (44%), N2 stage (59%), and detected in women (59%), compared with MMR-proficient tumors without BRAFV600E or KRAS mutations (33%, 19%, 41%, and 42%, respectively; all P <.0001). A significantly lower proportion of patients with MMR-proficient tumors with mutant BRAF (hazard ratio = 1.43; 95% confidence interval: 1.11-1.85; Padjusted =.0065) or mutant KRAS (hazard ratio = 1.48; 95% confidence interval: 1.27-1.74; Padjusted <.0001) survived disease-free for 5 years compared with patients whose MMR-proficient tumors lacked mutations in either gene. Disease-free survival rates of patients with MMR-deficient sporadic or familial subtypes was similar to those of patients with MMR-proficient tumors without BRAF or KRAS mutations. The observed differences in survival rates of patients with different tumor subtypes were validated in an independent cohort. CONCLUSIONS: We identified subtypes of stage III colon cancer, based on detection of mutations in BRAF (V600E) or KRAS, and MMR status that show differences in clinical and pathologic features and disease-free survival. Patients with MMR-proficient tumors and BRAF or KRAS mutations had statistically shorter survival times than patients whose tumors lacked these mutations. The tumor subtype found in nearly half of the study cohort (MMR-proficient without BRAFV600E or KRAS mutations) had similar outcomes to those of patients with MMR-deficient cancers.

Original languageEnglish (US)
Pages (from-to)88-99
Number of pages12
JournalGastroenterology
Volume148
Issue number1
DOIs
StatePublished - Jan 1 2015

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DNA Mismatch Repair
Colonic Neoplasms
Mutation
Neoplasms
Disease-Free Survival
Survival Rate
Confidence Intervals
Adjuvant Chemotherapy
Proportional Hazards Models
Methylation

Keywords

  • Colorectal Cancer
  • Genetics
  • Oncogene
  • Prognostic Factor

ASJC Scopus subject areas

  • Gastroenterology

Cite this

Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes. / Sinicrope, Frank A; Shi, Qian D; Smyrk, Thomas Christopher; Thibodeau, Stephen N; Dienstmann, Rodrigo; Guinney, Justin; Bot, Brian M.; Tejpar, Sabine; Delorenzi, Mauro; Goldberg, Richard M.; Mahoney, Michelle; Sargent, Daniel J.; Alberts, Steven Robert.

In: Gastroenterology, Vol. 148, No. 1, 01.01.2015, p. 88-99.

Research output: Contribution to journalArticle

Sinicrope, FA, Shi, QD, Smyrk, TC, Thibodeau, SN, Dienstmann, R, Guinney, J, Bot, BM, Tejpar, S, Delorenzi, M, Goldberg, RM, Mahoney, M, Sargent, DJ & Alberts, SR 2015, 'Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes', Gastroenterology, vol. 148, no. 1, pp. 88-99. https://doi.org/10.1053/j.gastro.2014.09.041
Sinicrope, Frank A ; Shi, Qian D ; Smyrk, Thomas Christopher ; Thibodeau, Stephen N ; Dienstmann, Rodrigo ; Guinney, Justin ; Bot, Brian M. ; Tejpar, Sabine ; Delorenzi, Mauro ; Goldberg, Richard M. ; Mahoney, Michelle ; Sargent, Daniel J. ; Alberts, Steven Robert. / Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes. In: Gastroenterology. 2015 ; Vol. 148, No. 1. pp. 88-99.
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abstract = "BACKGROUND & AIMS: Categorization of colon cancers into distinct subtypes using a combination of pathway-based biomarkers could provide insight into stage-independent variability in outcomes. METHODS: We used a polymerase chain reaction-based assay to detect mutations in BRAF (V600E) and in KRAS in 2720 stage III cancer samples, collected prospectively from patients participating in an adjuvant chemotherapy trial (NCCTG N0147). Tumors deficient or proficient in DNA mismatch repair (MMR) were identified based on detection of MLH1, MSH2, and MSH6 proteins and methylation of the MLH1 promoter. Findings were validated using tumor samples from a separate set of patients with stage III cancer (n = 783). Association with 5-year disease-free survival was evaluated using Cox proportional hazards models. RESULTS: Tumors were categorized into 5 subtypes based on MMR status and detection of BRAF or KRAS mutations which were mutually exclusive. Three subtypes were MMR proficient: those with mutations in BRAF (6.9{\%} of samples), mutations in KRAS (35{\%}), or tumors lacking either BRAF or KRAS mutations (49{\%}). Two subtypes were MMR deficient: the sporadic type (6.8{\%}) with BRAF mutation and/or or hypermethylation of MLH1 and the familial type (2.6{\%}), which lacked BRAFV600E or hypermethylation of MLH1. A higher percentage of MMR-proficient tumors with BRAFV600E were proximal (76{\%}), high-grade (44{\%}), N2 stage (59{\%}), and detected in women (59{\%}), compared with MMR-proficient tumors without BRAFV600E or KRAS mutations (33{\%}, 19{\%}, 41{\%}, and 42{\%}, respectively; all P <.0001). A significantly lower proportion of patients with MMR-proficient tumors with mutant BRAF (hazard ratio = 1.43; 95{\%} confidence interval: 1.11-1.85; Padjusted =.0065) or mutant KRAS (hazard ratio = 1.48; 95{\%} confidence interval: 1.27-1.74; Padjusted <.0001) survived disease-free for 5 years compared with patients whose MMR-proficient tumors lacked mutations in either gene. Disease-free survival rates of patients with MMR-deficient sporadic or familial subtypes was similar to those of patients with MMR-proficient tumors without BRAF or KRAS mutations. The observed differences in survival rates of patients with different tumor subtypes were validated in an independent cohort. CONCLUSIONS: We identified subtypes of stage III colon cancer, based on detection of mutations in BRAF (V600E) or KRAS, and MMR status that show differences in clinical and pathologic features and disease-free survival. Patients with MMR-proficient tumors and BRAF or KRAS mutations had statistically shorter survival times than patients whose tumors lacked these mutations. The tumor subtype found in nearly half of the study cohort (MMR-proficient without BRAFV600E or KRAS mutations) had similar outcomes to those of patients with MMR-deficient cancers.",
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TY - JOUR

T1 - Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes

AU - Sinicrope, Frank A

AU - Shi, Qian D

AU - Smyrk, Thomas Christopher

AU - Thibodeau, Stephen N

AU - Dienstmann, Rodrigo

AU - Guinney, Justin

AU - Bot, Brian M.

AU - Tejpar, Sabine

AU - Delorenzi, Mauro

AU - Goldberg, Richard M.

AU - Mahoney, Michelle

AU - Sargent, Daniel J.

AU - Alberts, Steven Robert

PY - 2015/1/1

Y1 - 2015/1/1

N2 - BACKGROUND & AIMS: Categorization of colon cancers into distinct subtypes using a combination of pathway-based biomarkers could provide insight into stage-independent variability in outcomes. METHODS: We used a polymerase chain reaction-based assay to detect mutations in BRAF (V600E) and in KRAS in 2720 stage III cancer samples, collected prospectively from patients participating in an adjuvant chemotherapy trial (NCCTG N0147). Tumors deficient or proficient in DNA mismatch repair (MMR) were identified based on detection of MLH1, MSH2, and MSH6 proteins and methylation of the MLH1 promoter. Findings were validated using tumor samples from a separate set of patients with stage III cancer (n = 783). Association with 5-year disease-free survival was evaluated using Cox proportional hazards models. RESULTS: Tumors were categorized into 5 subtypes based on MMR status and detection of BRAF or KRAS mutations which were mutually exclusive. Three subtypes were MMR proficient: those with mutations in BRAF (6.9% of samples), mutations in KRAS (35%), or tumors lacking either BRAF or KRAS mutations (49%). Two subtypes were MMR deficient: the sporadic type (6.8%) with BRAF mutation and/or or hypermethylation of MLH1 and the familial type (2.6%), which lacked BRAFV600E or hypermethylation of MLH1. A higher percentage of MMR-proficient tumors with BRAFV600E were proximal (76%), high-grade (44%), N2 stage (59%), and detected in women (59%), compared with MMR-proficient tumors without BRAFV600E or KRAS mutations (33%, 19%, 41%, and 42%, respectively; all P <.0001). A significantly lower proportion of patients with MMR-proficient tumors with mutant BRAF (hazard ratio = 1.43; 95% confidence interval: 1.11-1.85; Padjusted =.0065) or mutant KRAS (hazard ratio = 1.48; 95% confidence interval: 1.27-1.74; Padjusted <.0001) survived disease-free for 5 years compared with patients whose MMR-proficient tumors lacked mutations in either gene. Disease-free survival rates of patients with MMR-deficient sporadic or familial subtypes was similar to those of patients with MMR-proficient tumors without BRAF or KRAS mutations. The observed differences in survival rates of patients with different tumor subtypes were validated in an independent cohort. CONCLUSIONS: We identified subtypes of stage III colon cancer, based on detection of mutations in BRAF (V600E) or KRAS, and MMR status that show differences in clinical and pathologic features and disease-free survival. Patients with MMR-proficient tumors and BRAF or KRAS mutations had statistically shorter survival times than patients whose tumors lacked these mutations. The tumor subtype found in nearly half of the study cohort (MMR-proficient without BRAFV600E or KRAS mutations) had similar outcomes to those of patients with MMR-deficient cancers.

AB - BACKGROUND & AIMS: Categorization of colon cancers into distinct subtypes using a combination of pathway-based biomarkers could provide insight into stage-independent variability in outcomes. METHODS: We used a polymerase chain reaction-based assay to detect mutations in BRAF (V600E) and in KRAS in 2720 stage III cancer samples, collected prospectively from patients participating in an adjuvant chemotherapy trial (NCCTG N0147). Tumors deficient or proficient in DNA mismatch repair (MMR) were identified based on detection of MLH1, MSH2, and MSH6 proteins and methylation of the MLH1 promoter. Findings were validated using tumor samples from a separate set of patients with stage III cancer (n = 783). Association with 5-year disease-free survival was evaluated using Cox proportional hazards models. RESULTS: Tumors were categorized into 5 subtypes based on MMR status and detection of BRAF or KRAS mutations which were mutually exclusive. Three subtypes were MMR proficient: those with mutations in BRAF (6.9% of samples), mutations in KRAS (35%), or tumors lacking either BRAF or KRAS mutations (49%). Two subtypes were MMR deficient: the sporadic type (6.8%) with BRAF mutation and/or or hypermethylation of MLH1 and the familial type (2.6%), which lacked BRAFV600E or hypermethylation of MLH1. A higher percentage of MMR-proficient tumors with BRAFV600E were proximal (76%), high-grade (44%), N2 stage (59%), and detected in women (59%), compared with MMR-proficient tumors without BRAFV600E or KRAS mutations (33%, 19%, 41%, and 42%, respectively; all P <.0001). A significantly lower proportion of patients with MMR-proficient tumors with mutant BRAF (hazard ratio = 1.43; 95% confidence interval: 1.11-1.85; Padjusted =.0065) or mutant KRAS (hazard ratio = 1.48; 95% confidence interval: 1.27-1.74; Padjusted <.0001) survived disease-free for 5 years compared with patients whose MMR-proficient tumors lacked mutations in either gene. Disease-free survival rates of patients with MMR-deficient sporadic or familial subtypes was similar to those of patients with MMR-proficient tumors without BRAF or KRAS mutations. The observed differences in survival rates of patients with different tumor subtypes were validated in an independent cohort. CONCLUSIONS: We identified subtypes of stage III colon cancer, based on detection of mutations in BRAF (V600E) or KRAS, and MMR status that show differences in clinical and pathologic features and disease-free survival. Patients with MMR-proficient tumors and BRAF or KRAS mutations had statistically shorter survival times than patients whose tumors lacked these mutations. The tumor subtype found in nearly half of the study cohort (MMR-proficient without BRAFV600E or KRAS mutations) had similar outcomes to those of patients with MMR-deficient cancers.

KW - Colorectal Cancer

KW - Genetics

KW - Oncogene

KW - Prognostic Factor

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