Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer.

Ludovic Barault, Alessio Amatu, Giulia Siravegna, Agostino Ponzetti, Sebastian Moran, Andrea Cassingena, Benedetta Mussolin, Chiara Falcomata, Alexandra M. Binder, Carmen Cristiano, Daniele Oddo, Simonetta Guarrera, Carlotta Cancelliere, Sara Bustreo, Katia Bencardino, Sean Maden, Alice Vanzati, Patrizia Zavattari, Giuseppe Matullo, Mauro TruiniWilliam M. Grady, Patrizia Racca, Karin B. Michels, Salvatore Siena, Manel Esteller, Alberto Bardelli, Andrea Sartore-Bianchi, Federica Di Nicolantonio

Research output: Contribution to journalArticle

Abstract

OBJECTIVE: Mutations in cell-free circulating DNA (cfDNA) have been studied for tracking disease relapse in colorectal cancer (CRC). This approach requires personalised assay design due to the lack of universally mutated genes. In contrast, early methylation alterations are restricted to defined genomic loci allowing comprehensive assay design for population studies. Our objective was to identify cancer-specific methylated biomarkers which could be measured longitudinally in cfDNA (liquid biopsy) to monitor therapeutic outcome in patients with metastatic CRC (mCRC). DESIGN: Genome-wide methylation microarrays of CRC cell lines (n=149) identified five cancer-specific methylated loci (EYA4, GRIA4, ITGA4, MAP3K14-AS1, MSC). Digital PCR assays were employed to measure methylation of these genes in tumour tissue DNA (n=82) and cfDNA from patients with mCRC (n=182). Plasma longitudinal assessment was performed in a patient subset treated with chemotherapy or targeted therapy. RESULTS: Methylation in at least one marker was detected in all tumour tissue samples and in 156 mCRC patient cfDNA samples (85.7%). Plasma marker prevalence was 71.4% for EYA4, 68.5% for GRIA4, 69.7% for ITGA4, 69.1% for MAP3K14-AS1% and 65.1% for MSC. Dynamics of methylation markers was not affected by treatment type and correlated with objective tumour response and progression-free survival. CONCLUSION: This five-gene methylation panel can be used to circumvent the absence of patient-specific mutations for monitoring tumour burden dynamics in liquid biopsy under different therapeutic regimens. This method might be proposed for assessing pharmacodynamics in clinical trials or when conventional imaging has limitations.
Original languageEnglish
JournalGut
Publication statusPublished - Oct 1 2017

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Methylation
Colorectal Neoplasms
Biomarkers
DNA
Neoplasms
Therapeutics
Genes
Biopsy
Mutation
Tumor Burden
Disease-Free Survival
Clinical Trials
Genome
Recurrence
Drug Therapy
Cell Line
Polymerase Chain Reaction
Population

Keywords

  • chemotherapy, colorectal cancer, methylation, screening, tumour markers

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Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer. / Barault, Ludovic; Amatu, Alessio; Siravegna, Giulia; Ponzetti, Agostino; Moran, Sebastian; Cassingena, Andrea; Mussolin, Benedetta; Falcomata, Chiara; Binder, Alexandra M.; Cristiano, Carmen; Oddo, Daniele; Guarrera, Simonetta; Cancelliere, Carlotta; Bustreo, Sara; Bencardino, Katia; Maden, Sean; Vanzati, Alice; Zavattari, Patrizia; Matullo, Giuseppe; Truini, Mauro; Grady, William M.; Racca, Patrizia; Michels, Karin B.; Siena, Salvatore; Esteller, Manel; Bardelli, Alberto; Sartore-Bianchi, Andrea; Di Nicolantonio, Federica.

In: Gut, 01.10.2017.

Research output: Contribution to journalArticle

Barault, L, Amatu, A, Siravegna, G, Ponzetti, A, Moran, S, Cassingena, A, Mussolin, B, Falcomata, C, Binder, AM, Cristiano, C, Oddo, D, Guarrera, S, Cancelliere, C, Bustreo, S, Bencardino, K, Maden, S, Vanzati, A, Zavattari, P, Matullo, G, Truini, M, Grady, WM, Racca, P, Michels, KB, Siena, S, Esteller, M, Bardelli, A, Sartore-Bianchi, A & Di Nicolantonio, F 2017, 'Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer.', Gut.
Barault, Ludovic ; Amatu, Alessio ; Siravegna, Giulia ; Ponzetti, Agostino ; Moran, Sebastian ; Cassingena, Andrea ; Mussolin, Benedetta ; Falcomata, Chiara ; Binder, Alexandra M. ; Cristiano, Carmen ; Oddo, Daniele ; Guarrera, Simonetta ; Cancelliere, Carlotta ; Bustreo, Sara ; Bencardino, Katia ; Maden, Sean ; Vanzati, Alice ; Zavattari, Patrizia ; Matullo, Giuseppe ; Truini, Mauro ; Grady, William M. ; Racca, Patrizia ; Michels, Karin B. ; Siena, Salvatore ; Esteller, Manel ; Bardelli, Alberto ; Sartore-Bianchi, Andrea ; Di Nicolantonio, Federica. / Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer. In: Gut. 2017.
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abstract = "OBJECTIVE: Mutations in cell-free circulating DNA (cfDNA) have been studied for tracking disease relapse in colorectal cancer (CRC). This approach requires personalised assay design due to the lack of universally mutated genes. In contrast, early methylation alterations are restricted to defined genomic loci allowing comprehensive assay design for population studies. Our objective was to identify cancer-specific methylated biomarkers which could be measured longitudinally in cfDNA (liquid biopsy) to monitor therapeutic outcome in patients with metastatic CRC (mCRC). DESIGN: Genome-wide methylation microarrays of CRC cell lines (n=149) identified five cancer-specific methylated loci (EYA4, GRIA4, ITGA4, MAP3K14-AS1, MSC). Digital PCR assays were employed to measure methylation of these genes in tumour tissue DNA (n=82) and cfDNA from patients with mCRC (n=182). Plasma longitudinal assessment was performed in a patient subset treated with chemotherapy or targeted therapy. RESULTS: Methylation in at least one marker was detected in all tumour tissue samples and in 156 mCRC patient cfDNA samples (85.7{\%}). Plasma marker prevalence was 71.4{\%} for EYA4, 68.5{\%} for GRIA4, 69.7{\%} for ITGA4, 69.1{\%} for MAP3K14-AS1{\%} and 65.1{\%} for MSC. Dynamics of methylation markers was not affected by treatment type and correlated with objective tumour response and progression-free survival. CONCLUSION: This five-gene methylation panel can be used to circumvent the absence of patient-specific mutations for monitoring tumour burden dynamics in liquid biopsy under different therapeutic regimens. This method might be proposed for assessing pharmacodynamics in clinical trials or when conventional imaging has limitations.",
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TY - JOUR

T1 - Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer.

AU - Barault, Ludovic

AU - Amatu, Alessio

AU - Siravegna, Giulia

AU - Ponzetti, Agostino

AU - Moran, Sebastian

AU - Cassingena, Andrea

AU - Mussolin, Benedetta

AU - Falcomata, Chiara

AU - Binder, Alexandra M.

AU - Cristiano, Carmen

AU - Oddo, Daniele

AU - Guarrera, Simonetta

AU - Cancelliere, Carlotta

AU - Bustreo, Sara

AU - Bencardino, Katia

AU - Maden, Sean

AU - Vanzati, Alice

AU - Zavattari, Patrizia

AU - Matullo, Giuseppe

AU - Truini, Mauro

AU - Grady, William M.

AU - Racca, Patrizia

AU - Michels, Karin B.

AU - Siena, Salvatore

AU - Esteller, Manel

AU - Bardelli, Alberto

AU - Sartore-Bianchi, Andrea

AU - Di Nicolantonio, Federica

PY - 2017/10/1

Y1 - 2017/10/1

N2 - OBJECTIVE: Mutations in cell-free circulating DNA (cfDNA) have been studied for tracking disease relapse in colorectal cancer (CRC). This approach requires personalised assay design due to the lack of universally mutated genes. In contrast, early methylation alterations are restricted to defined genomic loci allowing comprehensive assay design for population studies. Our objective was to identify cancer-specific methylated biomarkers which could be measured longitudinally in cfDNA (liquid biopsy) to monitor therapeutic outcome in patients with metastatic CRC (mCRC). DESIGN: Genome-wide methylation microarrays of CRC cell lines (n=149) identified five cancer-specific methylated loci (EYA4, GRIA4, ITGA4, MAP3K14-AS1, MSC). Digital PCR assays were employed to measure methylation of these genes in tumour tissue DNA (n=82) and cfDNA from patients with mCRC (n=182). Plasma longitudinal assessment was performed in a patient subset treated with chemotherapy or targeted therapy. RESULTS: Methylation in at least one marker was detected in all tumour tissue samples and in 156 mCRC patient cfDNA samples (85.7%). Plasma marker prevalence was 71.4% for EYA4, 68.5% for GRIA4, 69.7% for ITGA4, 69.1% for MAP3K14-AS1% and 65.1% for MSC. Dynamics of methylation markers was not affected by treatment type and correlated with objective tumour response and progression-free survival. CONCLUSION: This five-gene methylation panel can be used to circumvent the absence of patient-specific mutations for monitoring tumour burden dynamics in liquid biopsy under different therapeutic regimens. This method might be proposed for assessing pharmacodynamics in clinical trials or when conventional imaging has limitations.

AB - OBJECTIVE: Mutations in cell-free circulating DNA (cfDNA) have been studied for tracking disease relapse in colorectal cancer (CRC). This approach requires personalised assay design due to the lack of universally mutated genes. In contrast, early methylation alterations are restricted to defined genomic loci allowing comprehensive assay design for population studies. Our objective was to identify cancer-specific methylated biomarkers which could be measured longitudinally in cfDNA (liquid biopsy) to monitor therapeutic outcome in patients with metastatic CRC (mCRC). DESIGN: Genome-wide methylation microarrays of CRC cell lines (n=149) identified five cancer-specific methylated loci (EYA4, GRIA4, ITGA4, MAP3K14-AS1, MSC). Digital PCR assays were employed to measure methylation of these genes in tumour tissue DNA (n=82) and cfDNA from patients with mCRC (n=182). Plasma longitudinal assessment was performed in a patient subset treated with chemotherapy or targeted therapy. RESULTS: Methylation in at least one marker was detected in all tumour tissue samples and in 156 mCRC patient cfDNA samples (85.7%). Plasma marker prevalence was 71.4% for EYA4, 68.5% for GRIA4, 69.7% for ITGA4, 69.1% for MAP3K14-AS1% and 65.1% for MSC. Dynamics of methylation markers was not affected by treatment type and correlated with objective tumour response and progression-free survival. CONCLUSION: This five-gene methylation panel can be used to circumvent the absence of patient-specific mutations for monitoring tumour burden dynamics in liquid biopsy under different therapeutic regimens. This method might be proposed for assessing pharmacodynamics in clinical trials or when conventional imaging has limitations.

KW - chemotherapy, colorectal cancer, methylation, screening, tumour markers

M3 - Article

JO - Gut

JF - Gut

SN - 0017-5749

ER -