High performance methylated DNA markers for detection of colon adenocarcinoma.
Colon adenocarcinoma
Detection
Liquid biopsy
Methylation
QM-MSP
cMethDNA
Journal
Clinical epigenetics
ISSN: 1868-7083
Titre abrégé: Clin Epigenetics
Pays: Germany
ID NLM: 101516977
Informations de publication
Date de publication:
13 12 2021
13 12 2021
Historique:
received:
15
09
2021
accepted:
29
11
2021
entrez:
14
12
2021
pubmed:
15
12
2021
medline:
1
2
2022
Statut:
epublish
Résumé
Colon cancer (CC) is treatable if detected in its early stages. Improved CC detection assays that are highly sensitive, specific, and available at point of care are needed. In this study, we systematically selected and tested methylated markers that demonstrate high sensitivity and specificity for detection of CC in tissue and circulating cell-free DNA. Hierarchical analysis of 22 candidate CpG loci was conducted using The Cancer Genome Atlas (TCGA) COAD 450K HumanMethylation database. Methylation of 13 loci was analyzed using quantitative multiplex methylation-specific PCR (QM-MSP) in a training set of fresh frozen colon tissues (N = 53). Hypermethylated markers were identified that were highest in cancer and lowest in normal colon tissue using the 75th percentile in Mann-Whitney analyses and the receiver operating characteristic (ROC) statistic. The cumulative methylation status of the marker panel was assayed in an independent test set of fresh frozen colon tissues (N = 52) using conditions defined and locked in the training set. A minimal marker panel of 6 genes was defined based on ROC area under the curve (AUC). Plasma samples (N = 20 colorectal cancers, stage IV and N = 20 normal) were tested by cMethDNA assay to evaluate marker performance in liquid biopsy. In the test set of samples, compared to normal tissue, a 6-gene panel showed 100% sensitivity and 90% specificity for detection of CC, and an AUC of 1.00 (95% CI 1.00, 1.00). In stage IV colorectal cancer plasma versus normal, an 8-gene panel showed 95% sensitivity, 100% specificity, and an AUC of 0.996 (95% CI 0.986, 1.00) while a 5-gene subset showed 100% sensitivity, 100% specificity, and an AUC of 1.00 (95% CI 1.00, 1.00), highly concordant with our observations in tissue. We identified high performance methylated DNA marker panels for detection of CC. This knowledge has set the stage for development and implementation of novel, automated, self-contained CC detection assays in tissue and blood which can expeditiously and accurately detect colon cancer in both developed and underdeveloped regions of the world, enabling optimal use of limited resources in low- and middle-income countries.
Sections du résumé
BACKGROUND
Colon cancer (CC) is treatable if detected in its early stages. Improved CC detection assays that are highly sensitive, specific, and available at point of care are needed. In this study, we systematically selected and tested methylated markers that demonstrate high sensitivity and specificity for detection of CC in tissue and circulating cell-free DNA.
METHODS
Hierarchical analysis of 22 candidate CpG loci was conducted using The Cancer Genome Atlas (TCGA) COAD 450K HumanMethylation database. Methylation of 13 loci was analyzed using quantitative multiplex methylation-specific PCR (QM-MSP) in a training set of fresh frozen colon tissues (N = 53). Hypermethylated markers were identified that were highest in cancer and lowest in normal colon tissue using the 75th percentile in Mann-Whitney analyses and the receiver operating characteristic (ROC) statistic. The cumulative methylation status of the marker panel was assayed in an independent test set of fresh frozen colon tissues (N = 52) using conditions defined and locked in the training set. A minimal marker panel of 6 genes was defined based on ROC area under the curve (AUC). Plasma samples (N = 20 colorectal cancers, stage IV and N = 20 normal) were tested by cMethDNA assay to evaluate marker performance in liquid biopsy.
RESULTS
In the test set of samples, compared to normal tissue, a 6-gene panel showed 100% sensitivity and 90% specificity for detection of CC, and an AUC of 1.00 (95% CI 1.00, 1.00). In stage IV colorectal cancer plasma versus normal, an 8-gene panel showed 95% sensitivity, 100% specificity, and an AUC of 0.996 (95% CI 0.986, 1.00) while a 5-gene subset showed 100% sensitivity, 100% specificity, and an AUC of 1.00 (95% CI 1.00, 1.00), highly concordant with our observations in tissue.
CONCLUSIONS
We identified high performance methylated DNA marker panels for detection of CC. This knowledge has set the stage for development and implementation of novel, automated, self-contained CC detection assays in tissue and blood which can expeditiously and accurately detect colon cancer in both developed and underdeveloped regions of the world, enabling optimal use of limited resources in low- and middle-income countries.
Identifiants
pubmed: 34903270
doi: 10.1186/s13148-021-01206-2
pii: 10.1186/s13148-021-01206-2
pmc: PMC8670296
doi:
Substances chimiques
Biomarkers, Tumor
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
218Subventions
Organisme : NCI NIH HHS
ID : P50 CA062924
Pays : United States
Informations de copyright
© 2021. The Author(s).
Références
Tech Coloproctol. 2018 Jul;22(7):481-498
pubmed: 30022330
Gut. 2007 Nov;56(11):1585-9
pubmed: 17591622
Cancers (Basel). 2021 Oct 01;13(19):
pubmed: 34638440
Cancer. 2010 Feb 1;116(3):544-73
pubmed: 19998273
World J Gastroenterol. 2017 May 28;23(20):3632-3642
pubmed: 28611516
Nat Clin Pract Oncol. 2005 Dec;2 Suppl 1:S4-11
pubmed: 16341240
CA Cancer J Clin. 2009 Nov-Dec;59(6):366-78
pubmed: 19897840
Crit Rev Oncol Hematol. 2016 Mar;99:74-80
pubmed: 26702883
CA Cancer J Clin. 2021 Jan;71(1):7-33
pubmed: 33433946
Dis Markers. 2007;23(1-2):51-71
pubmed: 17325426
Cancer Res. 2004 Jul 1;64(13):4442-52
pubmed: 15231653
N Engl J Med. 2014 Apr 3;370(14):1287-97
pubmed: 24645800
CA Cancer J Clin. 2018 Nov;68(6):394-424
pubmed: 30207593
Cancer Res. 2017 Jul 15;77(14):3814-3822
pubmed: 28512242
Cancer Res. 2014 Apr 15;74(8):2160-70
pubmed: 24737128
Gut. 2015 Oct;64(10):1637-49
pubmed: 26041752
Eur J Gastroenterol Hepatol. 2006 Apr;18(4):427-33
pubmed: 16538116
Best Pract Res Clin Gastroenterol. 2007;21(6):1031-48
pubmed: 18070702
Clin Cancer Res. 2019 Nov 1;25(21):6357-6367
pubmed: 31300453
Cancer. 2010 Oct 15;116(20):4872-81
pubmed: 20597133
World J Gastroenterol. 2014 Apr 21;20(15):4230-43
pubmed: 24764661
Gene. 2019 Aug 20;710:333-340
pubmed: 31202904
N Engl J Med. 2016 Mar 17;374(11):1065-75
pubmed: 26981936
CA Cancer J Clin. 2017 May 6;67(3):177-193
pubmed: 28248415
Cancer. 2006 Oct 1;107(7):1624-33
pubmed: 16933324
Colorectal Dis. 2016 Jun;18(6):549-61
pubmed: 26998585
Gut. 2017 Apr;66(4):683-691
pubmed: 26818619
N Engl J Med. 1993 May 13;328(19):1365-71
pubmed: 8474513
Nature. 2018 Jul;559(7715):507-516
pubmed: 30046068
Gastroenterology. 2008 Oct;135(4):1079-99
pubmed: 18773902
NPJ Breast Cancer. 2021 Jul 7;7(1):89
pubmed: 34234148
Nat Rev Gastroenterol Hepatol. 2011 Oct 18;8(12):686-700
pubmed: 22009203
Methods Mol Biol. 2018;1708:473-496
pubmed: 29224159