|
1
|
Ye PP, Viens R, Shelburne KE, Langpap SS, Bower XS, Shi JJ, Zhou W, Wignall JC, Zhu JJ, Woodward BD, Husain H, Tsao DS, Atay O. Molecular counting enables accurate and precise quantification of methylated ctDNA for tumor-naive cancer therapy response monitoring. Sci Rep 2025; 15:5869. [PMID: 39966612 PMCID: PMC11836444 DOI: 10.1038/s41598-025-90013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2024] [Accepted: 02/10/2025] [Indexed: 02/20/2025] Open
Abstract
Personalized cancer treatment can significantly extend survival and improve quality of life for many patients, but accurate and real-time therapy response monitoring remains challenging. To overcome logistical and technical challenges associated with therapy response monitoring via imaging scans or assays that track the variant allele fraction (VAF) of somatic mutations in circulating tumor DNA (ctDNA), we developed a tumor-naive liquid biopsy assay that leverages Quantitative Counting Template (QCT) technology to accurately and precisely quantify methylated ctDNA (Northstar Response™). The assay achieves < 10% coefficient of variation at 1% tumor fraction, which is 2 × lower than tumor-naive, targeted-panel approaches using VAF. The assay accurately distinguishes 0.25% absolute changes in contrived tumor fraction (AUC > 0.94) and performs well in 12 solid tumor types. Finally, in a small cohort of patients with lung, colorectal, or pancreatic cancer, the assay detected changes in ctDNA methylation that correlate with clinical outcomes. With its precise quantification of ctDNA methylation, Northstar Response is a novel tool for therapy response monitoring with the potential to inform clinical decision making for cancer treatment.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Wen Zhou
- BillionToOne, Inc, Menlo Park, CA, USA
| | | | | | - Brian D Woodward
- University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Hatim Husain
- University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | | | | |
Collapse
|
|
2
|
Wang Q, Ma C, Yang B, Zheng W, Liu X, Jian G. Dysregulation of DNA methylation in colorectal cancer: biomarker, immune regulation, and therapeutic potential. Int Immunopharmacol 2025; 145:113766. [PMID: 39644791 DOI: 10.1016/j.intimp.2024.113766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Revised: 11/16/2024] [Accepted: 11/30/2024] [Indexed: 12/09/2024]
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide, with morbidity and mortality ranking third and second among all cancers, respectively. As a result of a sequence of genetic and DNA methylation alterations that gradually accumulate in the healthy colonic epithelium, colorectal adenomas and invasive adenocarcinomas eventually give rise to CRC. Global hypomethylation and promoter-specific DNA methylation are characteristics of CRC. The pathophysiological role of aberrant DNA methylation in malignant tumors has garnered significant interest in the last few decades. In addition, DNA methylation has been shown to play a critical role in influencing immune cell function and tumor immune evasion. This review summarizes the most recent research on DNA methylation changes in CRC, including the role of DNA methylation-related enzymes in CRC tumorigenesis and biomarkers for diagnosis, predictive and prognostic. Besides, we focus on the emerging potential of epigenetic interventions to enhance antitumor immune responses and improve the CRC clinical practice.
Collapse
Affiliation(s)
- Qin Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, China; Department of Pathology, Yong Yoo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Chen Ma
- School of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Bin Yang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Wenxin Zheng
- School of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Xinya Liu
- School of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Gu Jian
- School of Pharmacy, Southwest Minzu University, Chengdu, China
| |
Collapse
|
|
3
|
Dai L, Johnson-Buck A, Laird PW, Tewari M, Walter NG. Ultrasensitive Amplification-Free Quantification of a Methyl CpG-Rich Cancer Biomarker by Single-Molecule Kinetic Fingerprinting. Anal Chem 2024; 96:17209-17216. [PMID: 39425638 PMCID: PMC11648273 DOI: 10.1021/acs.analchem.4c03002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2024]
Abstract
The most well-studied epigenetic marker in humans is the 5-methyl modification of cytosine in DNA, which has great potential as a disease biomarker. Currently, quantification of DNA methylation relies heavily on bisulfite conversion followed by PCR amplification and NGS or microarray analysis. PCR is subject to potential bias in differential amplification of bisulfite-converted methylated versus unmethylated sequences. Here, we combine bisulfite conversion with single-molecule kinetic fingerprinting to develop an amplification-free assay for DNA methylation at the branched-chain amino acid transaminase 1 (BCAT1) promoter. Our assay selectively responds to methylated sequences with a limit of detection below 1 fM and a specificity of 99.9999%. Evaluating complex genomic DNA matrices, we reliably distinguish <5% DNA methylation at the BCAT1 promoter in whole blood DNA from completely unmethylated whole-genome amplified DNA. Taken together, these results demonstrate the feasibility and sensitivity of our amplification-free, single-molecule quantification approach to improve the early detection of methylated cancer DNA biomarkers.
Collapse
Affiliation(s)
- Liuhan Dai
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Muneesh Tewari
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
|
4
|
Mohamed FR, Rose A, Sheehan-Hennessy L, Pedersen SK, Cornthwaite K, Laven-Law G, Young GP, Symonds EL, Winter JM. A blood test measuring DNA methylation of BCAT1 and IKZF1 for detection of lung adenocarcinoma. Cancer Treat Res Commun 2024; 40:100838. [PMID: 39154541 DOI: 10.1016/j.ctarc.2024.100838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/01/2024] [Accepted: 08/06/2024] [Indexed: 08/20/2024]
Abstract
BACKGROUND Colorectal (CRC) and lung adenocarcinoma share many genetic and pathological similarities. A circulating tumor DNA (ctDNA) test for CRC may also be useful for detection of lung adenocarcinoma. This study determined if a methylated BCAT1/IKZF1 ctDNA test for CRC can be used for detection of lung adenocarcinoma. PATIENTS AND METHODS Circulating cell free DNA (ccfDNA) was extracted from plasma collected prospectively from healthy controls, patients in remission from CRC, patients with lung adenocarcinoma, and patients with isolated metastatic CRC lung lesions. Plasma ccfDNA was bisulfite converted and assessed for methylated BCAT1/IKZF1 by quantitative real-time PCR. Comparisons between the different patient groups for a positive ctDNA test (BCAT1 and/or IKZF1) and ctDNA levels (% of total ccfDNA), as well as any associations with clinicopathological and demographic features, were assessed. RESULTS Methylated BCAT1/IKZF1 ctDNA was detected in 18/39 (46.2 %) patients with lung adenocarcinoma, which was significantly (p < 0.001) higher compared to healthy controls (49/606; 8.1 %) and patients in remission from CRC (22/171, 12.9 %). Patients with stage III/IV lung adenocarcinoma had higher BCAT1/IKZF1 ctDNA positivity compared to stage I/II cases (68.2 % vs 17.7 %, p < 0.01), where a significantly higher proportion tested positive for methylated IKZF1 ctDNA alone (54.6 % vs 5.9 %, p < 0.001). There was no difference in BCAT1/IKZF1 ctDNA test positivity between patients with stage IV primary lung adenocarcinoma (n = 17) compared to lung-metastasising CRC cases (n = 17; 70.6 % v 64.3 %). CONCLUSION A ctDNA test measuring methylated BCAT1/IKZF1 can sensitively detect lung adenocarcinoma and may be a promising aid for detection of advanced disease. CLINICAL TRIAL REGISTRATIONS Australian and New Zealand Clinical Trials Registry, www.anzctr.org.au, ACTRN12616001138471, ACTRN12611000318987.
Collapse
Affiliation(s)
- Faridh Raja Mohamed
- Department of Respiratory Sleep Medicine and Ventilation, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Anand Rose
- Department of Respiratory Sleep Medicine and Ventilation, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Lorraine Sheehan-Hennessy
- Cancer Impact Program, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Susanne K Pedersen
- Cancer Impact Program, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Kathryn Cornthwaite
- Cancer Impact Program, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Geraldine Laven-Law
- Cancer Impact Program, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Graeme P Young
- Cancer Impact Program, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Erin L Symonds
- Cancer Impact Program, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia; Department of Gastroenterology and Hepatology, Flinders Medical Centre, Southern Adelaide Local Health Network, Bedford Park, SA, Australia
| | - Jean M Winter
- Cancer Impact Program, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.
| |
Collapse
|
|
5
|
Laven-Law G, Symonds EL, Winter JM, Chen G, Flight IH, Hughes-Barton D, Wilson CJ, Young GP. Comparing a fecal immunochemical test and circulating tumor DNA blood test for colorectal cancer screening adherence. J Gastroenterol Hepatol 2024; 39:1267-1276. [PMID: 38430185 DOI: 10.1111/jgh.16531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/20/2023] [Accepted: 02/08/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND AND AIM Colorectal cancer (CRC) screening programs are most effective at reducing disease incidence and mortality through sustained screening participation. A novel blood test modality is being explored for CRC screening, but it is unclear whether it will provide sustained screening participation. This study aimed to investigate whether a circulating tumor DNA (ctDNA) blood test improved CRC screening re-participation when compared with a fecal immunochemical test (FIT) and to define the predictors of sustained CRC screening in an Australian population. METHODS South Australians who initially participated in CRC screening using a ctDNA blood test (n = 36) or FIT (n = 547) were offered the same CRC screening test approximately 2 years later through an extended phase of a randomized controlled trial. Surveys collected demographic, psychosocial, and clinical information. Predictors of CRC screening re-participation were explored using chi-square, Wilcoxon tests, and logistic regression. RESULTS Participants offered a second ctDNA blood test were equally likely to re-participate in CRC screening as those who completed a FIT in the first round and who were offered the same test (61% vs 66% re-participation respectively, P = 0.6). CRC fatalism, health activation, and self-efficacy were associated with repeated screening participation. Test awareness was predictive of repeated FIT-based CRC screening. CONCLUSIONS Targeted interventions to improve CRC screening awareness and increase patient health activation may improve CRC screening adherence. A ctDNA blood test may be a suitable CRC screening option to maintain CRC screening adherence in people who do not participate in screening with FIT.
Collapse
Affiliation(s)
- Geraldine Laven-Law
- College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Erin L Symonds
- College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
- Department of Gastroenterology and Hepatology, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Jean M Winter
- College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Gang Chen
- Centre for Health Economics, Monash University, Caulfield East, Victoria, Australia
| | - Ingrid H Flight
- College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Donna Hughes-Barton
- College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Carlene J Wilson
- College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
- Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Graeme P Young
- College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| |
Collapse
|
|
6
|
Laven-Law G, Kichenadasse G, Young GP, Symonds EL, Winter JM. BCAT1, IKZF1 and SEPT9: methylated DNA biomarkers for detection of pan-gastrointestinal adenocarcinomas. Biomarkers 2024; 29:194-204. [PMID: 38644767 DOI: 10.1080/1354750x.2024.2340663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/01/2024] [Indexed: 04/23/2024]
Abstract
INTRODUCTION Methylated circulating tumour DNA (ctDNA) blood tests for BCAT1/IKZF1 (COLVERA) and SEPT9 (Epi proColon) are used to detect colorectal cancer (CRC). However, there are no ctDNA assays approved for other gastrointestinal adenocarcinomas. We aimed to characterize BCAT1, IKZF1 and SEPT9 methylation in different gastrointestinal adenocarcinoma and non-gastrointestinal tumours to determine if these validated CRC biomarkers might be useful for pan-gastrointestinal adenocarcinoma detection. METHODS Tissue DNA methylation data from colorectal (COAD, READ), gastroesophageal (ESCA, STAD), pancreatic (PAAD) and cholangiocarcinoma (CHOL) adenocarcinoma cohorts within The Cancer Genome Atlas were used for differential methylation analyses. Clinicodemographic predictors of BCAT1, IKZF1 and SEPT9 methylation, and the selectivity of hypermethylated BCAT1, IKZF1 and SEPT9 for colorectal adenocarcinomas in comparison to other cancers were each explored with beta regression. RESULTS Hypermethylated BCAT1, IKZF1 and SEPT9 were each differentially methylated in colorectal and gastroesophageal adenocarcinomas. IKZF1 was differentially methylated in pancreatic adenocarcinoma. Hypermethylated DNA biomarkers BCAT1, IKZF1 and SEPT9 were largely stable across different stages of disease and were highly selective for gastrointestinal adenocarcinomas relative to other cancer types. DISCUSSION Existing CRC methylated ctDNA blood tests for BCAT1/IKZF1 and SEPT9 might be usefully repurposed for use in other gastrointestinal adenocarcinomas and warrant further prospective ctDNA studies.
Collapse
Affiliation(s)
- Geraldine Laven-Law
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
| | - Ganessan Kichenadasse
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
- Department of Medical Oncology, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, South Australia
| | - Graeme P Young
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
| | - Erin L Symonds
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
- Department of Gastroenterology and Hepatology, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, South Australia
| | - Jean M Winter
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
| |
Collapse
|
|
7
|
Dai L, Johnson-Buck A, Laird PW, Tewari M, Walter NG. Ultrasensitive amplification-free quantification of a methyl CpG-rich cancer biomarker by single-molecule kinetic fingerprinting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.587997. [PMID: 38645159 PMCID: PMC11030368 DOI: 10.1101/2024.04.06.587997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The most well-studied epigenetic marker in humans is the 5-methyl modification of cytosine in DNA, which has great potential as a disease biomarker in liquid biopsies of cell-free DNA. Currently, quantification of DNA methylation relies heavily on bisulfite conversion followed by PCR amplification and NGS or microarray analysis. PCR is subject to potential bias in differential amplification of bisulfite-converted methylated versus unmethylated sequences. Here, we combine bisulfite conversion with single-molecule kinetic fingerprinting to develop an amplification-free assay for DNA methylation at the branched-chain amino acid transaminase 1 (BCAT1) promoter. Our assay selectively responds to methylated sequences with a limit of detection below 1 fM and a specificity of 99.9999%. Evaluating complex genomic DNA matrices, we reliably distinguish 2-5% DNA methylation at the BCAT1 promoter in whole blood DNA from completely unmethylated whole-genome amplified DNA. Taken together, these results demonstrate the feasibility and sensitivity of our amplification-free, single-molecule quantification approach to improve the early detection of methylated cancer DNA biomarkers.
Collapse
Affiliation(s)
- Liuhan Dai
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Muneesh Tewari
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
|
8
|
Ye J, Zhang J, Ding W. DNA methylation modulates epigenetic regulation in colorectal cancer diagnosis, prognosis and precision medicine. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:34-53. [PMID: 38464391 PMCID: PMC10918240 DOI: 10.37349/etat.2024.00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/11/2023] [Indexed: 03/12/2024] Open
Abstract
Colorectal cancer (CRC) is a multifaceted disease influenced by the interplay of genetic and environmental factors. The clinical heterogeneity of CRC cannot be attributed exclusively to genetic diversity and environmental exposures, and epigenetic markers, especially DNA methylation, play a critical role as key molecular markers of cancer. This review compiles a comprehensive body of evidence underscoring the significant involvement of DNA methylation modifications in the pathogenesis of CRC. Moreover, this review explores the potential utility of DNA methylation in cancer diagnosis, prognostics, assessment of disease activity, and prediction of drug responses. Recognizing the impact of DNA methylation will enhance the ability to identify distinct CRC subtypes, paving the way for personalized treatment strategies and advancing precision medicine in the management of CRC.
Collapse
Affiliation(s)
- Jingxin Ye
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
- Department of Gastroenterology, The Affiliated Suqian Hospital of Xuzhou Medical University, Suqian 223800, Jiangsu Province, China
| | - Jianfeng Zhang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Weifeng Ding
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| |
Collapse
|
|
9
|
Xu K, Yu AR, Pan SB, He J. Diagnostic value of methylated branched chain amino acid transaminase 1/IKAROS family zinc finger 1 for colorectal cancer. World J Gastroenterol 2023; 29:5240-5253. [PMID: 37901447 PMCID: PMC10600955 DOI: 10.3748/wjg.v29.i36.5240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND The diagnostic value of combined methylated branched chain amino acid transaminase 1 (BCAT1)/IKAROS family zinc finger 1 (IKZF1) in plasma for colorectal cancer (CRC) has been explored since 2015. Recently, several related studies have published their results and showed its diagnostic efficacy. AIM To analyze the diagnostic value of methylated BCAT1/IKZF1 in plasma for screening and postoperative follow-up of CRC. METHODS The candidate studies were identified by searching the PubMed, Embase, Cochrane Library, CNKI, and Wanfang databases from May 31, 2003 to June 1, 2023. Sensitivity, specificity, and diagnostic accuracy were calculated by merging ratios or means. RESULTS Twelve eligible studies were included in the analysis, involving 6561 participants. The sensitivity of methylated BCAT1/IKZF1 in plasma for CRC diagnosis was 60% [95% confidence interval (CI) 53-67] and specificity was 92% (95%CI: 90-94). The positive and negative likelihood ratios were 8.0 (95%CI: 5.8-11.0) and 0.43 (95%CI: 0.36-0.52), respectively. Diagnostic odds ratio was 19 (95%CI: 11-30) and area under the curve was 0.88 (95%CI: 0.85-0.91). The sensitivity and specificity for CRC screening were 64% (95%CI: 59-69) and 92% (95%CI: 91-93), respectively. The sensitivity and specificity for recurrence detection during follow-up were 54% (95%CI: 42-67) and 93% (95%CI: 88-96), respectively. CONCLUSION The detection of methylated BCAT1/IKZF1 in plasma, as a non-invasive detection method of circulating tumor DNA, has potential CRC diagnosis, but the clinical application prospect needs to be further explored.
Collapse
Affiliation(s)
- Ke Xu
- Clinical Medical College, Chengdu Medical College, Chengdu 610500, Sichuan Province, China
- Department of Oncology, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China
| | - Ai-Ru Yu
- Clinical Medical College, Chengdu Medical College, Chengdu 610500, Sichuan Province, China
- Department of Oncology, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China
| | - Shen-Bin Pan
- Clinical Medical College, Chengdu Medical College, Chengdu 610500, Sichuan Province, China
- Department of Oncology, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China
| | - Jie He
- Clinical Medical College, Chengdu Medical College, Chengdu 610500, Sichuan Province, China
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China
| |
Collapse
|
|
10
|
Zhao F, Bai P, Xu J, Li Z, Muhammad S, Li D, Zhang Z, Gao Y, Liu Q. Efficacy of cell-free DNA methylation-based blood test for colorectal cancer screening in high-risk population: a prospective cohort study. Mol Cancer 2023; 22:157. [PMID: 37770864 PMCID: PMC10538018 DOI: 10.1186/s12943-023-01866-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/21/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Although colonoscopy is the standard screening test for colorectal cancer (CRC), its use is limited by a poor compliance rate, the need for extensive bowel preparation, and the risk of complications. As an alternative, an FDA-approved stool-based DNA test, Cologuard, has demonstrated satisfactory detection performance for CRC, but its compliance rate remains suboptimal, primarily attributable to individuals' reluctance to provide stool samples. METHODS We developed a noninvasive blood-based CRC test, ColonSecure, based on cell-free DNA containing cancer-specific CpG island methylation patterns. We initially screened publicly available datasets for differentially methylated CpG sites in CRC with prediction potential. Subsequently, we performed two sequential bisulfite-free methylation sequencing on blood samples obtained from CRC patients and non-cancer controls. Through rigorous evaluation of each marker and machine learning-assisted feature selection, we identified 149 hypermethylated markers from over 193,000 CpG sites. These markers were then utilized to construct the ColonSecure model, enabling accurate CRC detection. RESULTS We validated the efficacy of our cell-free DNA methylation-based blood test for CRC screening with 3493 high-risk individuals identified from 114,136 urban residents. The ColonSecure test identified 89 out of 103 CRC patients diagnosed by the follow-up colonoscopy, outperforming CEA, CRP, and CA19-9 (with a sensitivity of 86.4% compared to 45.6%, 39.8%, and 25.2% for CEA, CRP, and CA19-9 respectively; an AUROC of 0.956 compared to an AUROC of < 0.77 for other methods). CONCLUSION Our observations emphasize the potential of our multiple cfDNA methylation marker-based test for CRC screening in high-risk populations.
Collapse
Affiliation(s)
- Fuqiang Zhao
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ping Bai
- Department of Operating Rooms, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianfeng Xu
- Laboratory for Advanced Medicine & Health Ltd. (LAMH), Beijing, 100176, China
| | - Zitong Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shan Muhammad
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Diange Li
- Laboratory for Advanced Medicine & Health Ltd. (LAMH), Beijing, 100176, China
| | - Zeyue Zhang
- Laboratory for Advanced Medicine & Health Ltd. (LAMH), Beijing, 100176, China
| | - Yibo Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- Laboratory of Translational Medicine, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- Central Laboratory & Shenzhen Key Laboratory of Epigenetics and Precision Medicine for Cancers, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China.
| | - Qian Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| |
Collapse
|
|
11
|
Petit J, Carroll G, Zhao J, Roper E, Pockney P, Scott RJ. Evaluation of epigenetic methylation biomarkers for the detection of colorectal cancer using droplet digital PCR. Sci Rep 2023; 13:8883. [PMID: 37264006 DOI: 10.1038/s41598-023-35631-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 05/21/2023] [Indexed: 06/03/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. Screening programs allow early diagnosis and have improved the clinical management of this disease. Aberrant DNA methylation is increasingly being explored as potential biomarkers for many types of cancers. In this study we investigate the methylation of ten target genes in 105 CRC and paired normal adjacent colonic tissue samples using a MethylLight droplet digital PCR (ML-ddPCR) assay. Receiver operator characteristic (ROC) curves were used to determine the diagnostic performance of all target genes individually and in combination. All 515 different combinations of genes showed significantly higher levels of methylation in CRC tissue. The combination of multiple target genes into a single test generally resulted in greater diagnostic accuracy when compared to single target genes. Our data confirms that ML-ddPCR is able to reliably detect significant differences in DNA methylation between CRC tissue and normal adjacent colonic tissue in a specific selection of target genes.
Collapse
Affiliation(s)
- J Petit
- Division of Surgery, John Hunter Hospital, New Lambton Heights, NSW, Australia.
- Hunter Medical Research Institute, Newcastle, Australia.
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.
| | - G Carroll
- Division of Surgery, John Hunter Hospital, New Lambton Heights, NSW, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, Newcastle, Australia
| | - J Zhao
- Division of Surgery, John Hunter Hospital, New Lambton Heights, NSW, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
| | - E Roper
- Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - P Pockney
- Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - R J Scott
- Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
- Pathology North, Newcastle, NSW, Australia
| |
Collapse
|
|
12
|
Mokhtari K, Peymani M, Rashidi M, Hushmandi K, Ghaedi K, Taheriazam A, Hashemi M. Colon cancer transcriptome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:49-82. [PMID: 37059270 DOI: 10.1016/j.pbiomolbio.2023.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Over the last four decades, methodological innovations have continuously changed transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples using RNA sequencing (RNA-seq). These transcriptomes serve as a connection between cellular behaviors and their underlying molecular mechanisms, such as mutations. This relationship, in the context of cancer, provides a chance to unravel tumor complexity and heterogeneity and uncover novel biomarkers or treatment options. Since colon cancer is one of the most frequent malignancies, its prognosis and diagnosis seem to be critical. The transcriptome technology is developing for an earlier and more accurate diagnosis of cancer which can provide better protectivity and prognostic utility to medical teams and patients. A transcriptome is a whole set of expressed coding and non-coding RNAs in an individual or cell population. The cancer transcriptome includes RNA-based changes. The combined genome and transcriptome of a patient may provide a comprehensive picture of their cancer, and this information is beginning to affect treatment decision-making in real-time. A full assessment of the transcriptome of colon (colorectal) cancer has been assessed in this review paper based on risk factors such as age, obesity, gender, alcohol use, race, and also different stages of cancer, as well as non-coding RNAs like circRNAs, miRNAs, lncRNAs, and siRNAs. Similarly, they have been examined independently in the transcriptome study of colon cancer.
Collapse
Affiliation(s)
- Khatere Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| |
Collapse
|
|
13
|
Min L, Chen J, Yu M, Liu D. Using Circulating Tumor DNA as a Novel Biomarker to Screen and Diagnose Colorectal Cancer: A Meta-Analysis. J Clin Med 2023; 12:408. [PMID: 36675337 PMCID: PMC9860998 DOI: 10.3390/jcm12020408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/27/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
(1) Background: Circulating tumor DNA (ctDNA) has emerged as a promising biomarker for many kinds of tumors. However, whether ctDNA could be an accurate diagnostic biomarker in colorectal cancer (CRC) remains to be clarified. The aim of this study was to evaluate the diagnostic accuracy of ctDNA in CRC. (2) Methods: PubMed, Web of Science, and Cochrane databases were searched to identify studies reporting the use of ctDNA to screen and diagnose CRC, and all relevant studies published until October 2022 were enrolled for our analysis. These studies were divided into three primer subgroups: the subgroup of quantitative or qualitative analysis of ctDNA and the subgroup of septin9 (SEPT9) methylation assay. (3) Results: A total of 79 qualified articles with 25,240 subjects were incorporated into our meta-analysis. For quantitative studies, the combined sensitivity (SEN), specificity (SPE), and diagnostic odds ratio (DOR) were 0.723 (95% CI: 0.623-0.803), 0.920 (95% CI: 0.827-0.966), and 23.305 (95% CI: 9.378-57.906), respectively, yielding an AUC of 0.860. The corresponding values for qualitative studies were 0.610 (95% CI: 0.566-0.651), 0.891 (95% CI: 0.878-0.909), 12.569 (95% CI: 9.969-15.848), and 0.823, respectively. Detection of SEPT9 methylation depicted an AUC of 0.879, with an SEN of 0.679 (95% CI: 0.622-0.732), an SPE of 0.903 (95% CI: 0.878-0.923), and a DOR of 20.121 (95% CI:14.404-28.106), respectively. (4) Conclusion: Blood-based ctDNA assay would be a potential novel biomarker for CRC screening and diagnosis. Specifically, quantitative analysis of ctDNA or qualitative analysis of SEPT9 methylation exhibited satisfying diagnostic efficiency. Larger sample studies are needed to further confirm our conclusions and to make the ctDNA approach more sensitive and specific.
Collapse
Affiliation(s)
- Liang Min
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha 410011, China
- Research Center of Digestive Disease, Central South University, Changsha 410011, China
| | - Jinghua Chen
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Meihong Yu
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha 410011, China
- Research Center of Digestive Disease, Central South University, Changsha 410011, China
| | - Deliang Liu
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha 410011, China
- Research Center of Digestive Disease, Central South University, Changsha 410011, China
| |
Collapse
|
|
14
|
Yang M, Sun M, Zhang H. The Interaction Between Epigenetic Changes, EMT, and Exosomes in Predicting Metastasis of Colorectal Cancers (CRC). Front Oncol 2022; 12:879848. [PMID: 35712512 PMCID: PMC9197117 DOI: 10.3389/fonc.2022.879848] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/01/2022] [Indexed: 12/12/2022] Open
Abstract
Worldwide, colorectal cancer (CRC) ranks as the third most common malignancy, and the second most deadly with nearly one million attributable deaths in 2020. Metastatic disease is present in nearly 25% of newly diagnosed CRC, and despite advances in chemotherapy, less than 20% will remain alive at 5 years. Epigenetic change plays a key role in the epithelial-to-mesenchymal transition (EMT), which is a crucial phenotype for metastasis and mainly includes DNA methylation, non-coding RNAs (ncRNAs), and N6-methyladenosine (m6A) RNA, seemingly valuable biomarkers in CRCs. For ncRNAs, there exists a “molecular sponge effect” between long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs). The detection of exosomes is a novel method in CRC monitoring, especially for predicting metastasis. There is a close relationship between exosomes and EMT in CRCs. This review summarizes the close relationship between epigenetic changes and EMT in CRCs and emphasizes the crucial function of exosomes in regulating the EMT process.
Collapse
|
|
15
|
Müller D, Győrffy B. DNA methylation-based diagnostic, prognostic, and predictive biomarkers in colorectal cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188722. [PMID: 35307512 DOI: 10.1016/j.bbcan.2022.188722] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/21/2022] [Accepted: 03/13/2022] [Indexed: 12/12/2022]
Abstract
DNA methylation is an epigenetic mechanism regulating gene expression. Changes in DNA methylation were suggested to be useful biomarkers for diagnosis, and for the determination of prognosis and treatment response. Here, we provide an overview of methylation-based biomarkers in colorectal cancer. First, we start with the two methylation-based diagnostic biomarkers already approved for colorectal cancer, SEPT9 and the combination of NDRG4 and BMP3. Then, we provide a list-based overview of new biomarker candidates depending on the sample source including plasma, stool, urine, and surgically removed tumor tissues. The most often identified markers like SDC2, VIM, APC, MGMT, SFRP1, SFRP2, and NDRG4 have distinct functions previously linked to tumor progression. Although numerous studies have identified tumor-specific methylation changes, most of these alterations were observed in a single study only. The lack of validation in independent samples means low reproducibility and is a major limitation. The genome-wide determination of methylation status (methylome) can provide data to solve these issues. In the third section of the review, methylome studies focusing on different aspects related to CRC, including precancerous lesions, CRC-specific changes, molecular subtypes, aging, and chemotherapy response are summarized. Notably, techniques simultaneously analyzing a large set of regions can also uncover epigenetic regulation of genes which have not yet been associated with tumorigenesis previously. A remaining constraint of studies published to date is the low patient number utilized in these preventing the identification of clinically valuable biomarker candidates. Either future large-scale studies or the integration of already available methylome-level data will be necessary to uncover biomarkers sufficiently robust for clinical application.
Collapse
Affiliation(s)
- Dalma Müller
- Dept. of Bioinformatics, Semmelweis University, Budapest, Hungary; Cancer Biomarker Research Group, RCNS, Budapest, Hungary
| | - Balázs Győrffy
- Dept. of Bioinformatics, Semmelweis University, Budapest, Hungary; Cancer Biomarker Research Group, RCNS, Budapest, Hungary.
| |
Collapse
|
|
16
|
Vatandoust S, Wattchow D, Sposato L, Michael MZ, Leung J, Gormly K, Chen G, Symonds EL, Tie J, Papanicolas LE, Woods S, Gebski V, Mead K, Kuruni A, Karapetis CS. A longitudinal cohort study of watch and wait in complete clinical responders after chemo-radiotherapy for localised rectal cancer: study protocol. BMC Cancer 2022; 22:222. [PMID: 35232427 PMCID: PMC8887187 DOI: 10.1186/s12885-022-09304-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/16/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Rectal Cancer is a common malignancy. The current treatment approach for patients with locally advanced rectal cancer involves neoadjuvant chemoradiotherapy followed by surgical resection of the rectum. The resection can lead to complications and long-term consequences. A clinical complete response is observed in some patients after chemoradiotherapy. A number of recent studies have shown that patients can be observed safely after completing chemoradiotherapy (without surgery), provided clinical complete response has been achieved. In this approach, resection is reserved for cases of regrowth. This is called the watch and wait approach. This approach potentially avoids unnecessary surgical resection of the rectum and the resulting complications. In this study, we will prospectively investigate this approach. METHODS Adult patients with a diagnosis of rectal cancer planned to receive neoadjuvant long course chemoradiotherapy (± subsequent combination chemotherapy) will be consented into the study prior to commencing treatment. After completing the chemoradiotherapy (± subsequent combination chemotherapy), based on the clinical response, subjects will be allocated to one of the following arms: subjects who achieved a clinical complete response will be allocated to the watch and wait arm and others to the standard management arm (which includes resection). The aim of the study is to determine the rate of local failure and other safety and efficacy outcomes in the watch and wait arm. Patient reported outcome measures and the use of biomarkers as part of the clinical monitoring will be studied in both arms of the study. DISCUSSION This study will prospectively investigate the safety of the watch and wait approach. We will investigate predictive biomarkers (molecular biomarkers and imaging biomarkers) and patient reported outcome measures in the study population and the cost effectiveness of the watch and wait approach. This study will also help evaluate a defined monitoring schedule for patients managed with the watch and wait approach. This protocol covers the first two years of follow up, we are planning a subsequent study which covers year 3-5 follow up for the study population. TRIAL REGISTRATION Name of the registry: Australia and New Zealand Clinical Trials Registry (ANZCTR). TRIAL REGISTRATION NUMBER Trial ID: ACTRN12619000207112 Registered 13 February 2019, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=376810.
Collapse
Affiliation(s)
- Sina Vatandoust
- Flinders Medical Centre, Adelaide, Australia.
- Flinders Centre for Innovation in Cancer, Flinders University, Flinders Drive, Bedford Park, Adelaide, South Australia, 5042, Australia.
| | - David Wattchow
- Flinders Medical Centre, Adelaide, Australia
- Flinders Centre for Innovation in Cancer, Flinders University, Flinders Drive, Bedford Park, Adelaide, South Australia, 5042, Australia
| | - Luigi Sposato
- Flinders Medical Centre, Adelaide, Australia
- Flinders Centre for Innovation in Cancer, Flinders University, Flinders Drive, Bedford Park, Adelaide, South Australia, 5042, Australia
| | - Michael Z Michael
- Flinders Medical Centre, Adelaide, Australia
- Flinders Centre for Innovation in Cancer, Flinders University, Flinders Drive, Bedford Park, Adelaide, South Australia, 5042, Australia
| | - John Leung
- Flinders Medical Centre, Adelaide, Australia
- GenesisCare, Adelaide, Australia
| | - Kirsten Gormly
- Dr Jones & Partners Medical Imaging, Adelaide, Australia
- University of Adelaide, Adelaide, Australia
| | - Gang Chen
- Monash University, Melbourne, Australia
| | - Erin L Symonds
- Flinders Medical Centre, Adelaide, Australia
- Flinders Centre for Innovation in Cancer, Flinders University, Flinders Drive, Bedford Park, Adelaide, South Australia, 5042, Australia
| | - Jeanne Tie
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Peter MacCallum Cancer Centre, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Lito Electra Papanicolas
- Flinders Medical Centre, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Susan Woods
- University of Adelaide, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Val Gebski
- NHMRC Clinical Trials Centre, The University of Sydney, Sydney, Australia
| | - Kelly Mead
- Flinders Medical Centre, Adelaide, Australia
| | | | - Christos S Karapetis
- Flinders Medical Centre, Adelaide, Australia
- Flinders Centre for Innovation in Cancer, Flinders University, Flinders Drive, Bedford Park, Adelaide, South Australia, 5042, Australia
| |
Collapse
|
|
17
|
Winter J, Sheehan-Hennessy L, Yao B, Pedersen S, Wassie M, Eaton M, Chong M, Young G, Symonds E. Detection of hypermethylated BCAT1 and IKZF1 DNA in blood and tissues of colorectal, breast and prostate cancer patients. Cancer Biomark 2022; 34:493-503. [DOI: 10.3233/cbm-210399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND: Detection of circulating cell-free DNA (ccfDNA) methylated in BCAT1 and IKZF1 is a sensitive for detection of colorectal cancer (CRC), but it is not known if these biomarkers are present in other common adenocarcinomas. OBJECTIVE: Compare methylation levels of BCAT1 and IKZF1 in tissue and plasma from breast, prostate, and colorectal cancer patients. METHODS: Blood was collected from 290 CRC, 32 breast and 101 prostate cancer patients, and 606 cancer-free controls. Tumor and matched normal tissues were collected at surgery: 26 breast, 9 prostate and 15 CRC. DNA methylation in BCAT1 and IKZF1 was measured in blood and tissues. RESULTS: Either biomarker was detected in blood from 175/290 (60.3%) of CRC patients. The detection rate was higher than that measured in controls (48/606 (8.1%), OR = 18.2, 95%CI: 11.1–29.0). The test positivity rates in breast and prostate cancer patients were 9.4% (3/32) and 6.9% (7/101), respectively, and not significantly different to that measured in gender-matched controls (8.0% (33/382) females (OR = 0.84, 95%CI: 0.23–3.1) and 7.6% (26/318) males (OR = 0.86, 95%CI: 0.65–2.1). In tumor and non-neoplastic tissues, 93.5% (14/15) of CRC tumors were methylated in BCAT1 and/or IKZF1 (p< 0.004). Only 11.5% (3/26) and 44.4% (4/9) (p= 0.083) of breast and prostate tumors were hypermethylated in these two genes. CONCLUSIONS: Detection of circulating DNA methylated in BCAT1 and IKZF1 is sensitive and specific for CRC but not breast or prostate cancer.
Collapse
Affiliation(s)
- Jean M. Winter
- Cancer Research, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia, Australia
- Bowel Health Service, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Lorraine Sheehan-Hennessy
- Cancer Research, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia, Australia
- Bowel Health Service, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Beibei Yao
- Cancer Research, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia, Australia
| | | | - Molla M. Wassie
- Cancer Research, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia, Australia
- Bowel Health Service, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Michael Eaton
- Flinders Breast Cancer Unit, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Michael Chong
- Urology Services, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Graeme P. Young
- Cancer Research, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia, Australia
| | - Erin L. Symonds
- Cancer Research, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia, Australia
- Bowel Health Service, Flinders Medical Centre, Bedford Park, South Australia, Australia
| |
Collapse
|
|
18
|
Ionica E, Gaina G, Tica M, Chifiriuc MC, Gradisteanu-Pircalabioru G. Contribution of Epithelial and Gut Microbiome Inflammatory Biomarkers to the Improvement of Colorectal Cancer Patients' Stratification. Front Oncol 2022; 11:811486. [PMID: 35198435 PMCID: PMC8859258 DOI: 10.3389/fonc.2021.811486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022] Open
Abstract
In order to ensure that primary endpoints of clinical studies are attained, the patients' stratification is an important aspect. Selection criteria include age, gender, and also specific biomarkers, such as inflammation scores. These criteria are not sufficient to achieve a straightforward selection, however, in case of multifactorial diseases, with unknown or partially identified mechanisms, occasionally including host factors, and the microbiome. In these cases, the efficacy of interventions is difficult to predict, and as a result, the selection of subjects is often random. Colorectal cancer (CRC) is a highly heterogeneous disease, with variable clinical features, outcomes, and response to therapy; the CRC onset and progress involves multiple sequential steps with accumulation of genetic alterations, namely, mutations, gene amplification, and epigenetic changes. The gut microbes, either eubiotic or dysbiotic, could influence the CRC evolution through a complex and versatile crosstalk with the intestinal and immune cells, permanently changing the tumor microenvironment. There have been significant advances in the development of personalized approaches for CRC screening, treatment, and potential prevention. Advances in molecular techniques bring new criteria for patients' stratification-mutational analysis at the time of diagnosis to guide treatment, for example. Gut microbiome has emerged as the main trigger of gut mucosal homeostasis. This may impact cancer susceptibility through maintenance of the epithelial/mucus barrier and production of protective metabolites, such as short-chain fatty acids (SCFAs) via interactions with the hosts' diet and metabolism. Microbiome dysbiosis leads to the enrichment of cancer-promoting bacterial populations, loss of protective populations or maintaining an inflammatory chronic state, all of which contribute to the development and progression of CRC. Meanwhile, variations in patient responses to anti-cancer immuno- and chemotherapies were also linked to inter-individual differences in intestine microbiomes. The authors aim to highlight the contribution of epithelial and gut microbiome inflammatory biomarkers in the improvement of CRC patients' stratification towards a personalized approach of early diagnosis and treatment.
Collapse
Affiliation(s)
- Elena Ionica
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Gisela Gaina
- Laboratory of Cell Biology, Neuroscience and Experimental Miology, Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Mihaela Tica
- Bucharest Emergency University Hospital, Bucharest, Romania
| | - Mariana-Carmen Chifiriuc
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Biological Science Division, Romanian Academy of Sciences, Bucharest, Romania
| | | |
Collapse
|
|
19
|
Hitchins MP. Methylated circulating tumor DNA biomarkers for the blood-based detection of cancer signals. EPIGENETICS IN PRECISION MEDICINE 2022:471-512. [DOI: 10.1016/b978-0-12-823008-4.00001-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2025]
|
|
20
|
Angeles AK, Janke F, Bauer S, Christopoulos P, Riediger AL, Sültmann H. Liquid Biopsies beyond Mutation Calling: Genomic and Epigenomic Features of Cell-Free DNA in Cancer. Cancers (Basel) 2021; 13:5615. [PMID: 34830770 PMCID: PMC8616179 DOI: 10.3390/cancers13225615] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 01/12/2023] Open
Abstract
Cell-free DNA (cfDNA) analysis using liquid biopsies is a non-invasive method to gain insights into the biology, therapy response, mechanisms of acquired resistance and therapy escape of various tumors. While it is well established that individual cancer treatment options can be adjusted by panel next-generation sequencing (NGS)-based evaluation of driver mutations in cfDNA, emerging research additionally explores the value of deep characterization of tumor cfDNA genomics and fragmentomics as well as nucleosome modifications (chromatin structure), and methylation patterns (epigenomics) for comprehensive and multi-modal assessment of cfDNA. These tools have the potential to improve disease monitoring, increase the sensitivity of minimal residual disease identification, and detection of cancers at earlier stages. Recent progress in emerging technologies of cfDNA analysis is summarized, the added potential clinical value is highlighted, strengths and limitations are identified and compared with conventional targeted NGS analysis, and current challenges and future directions are discussed.
Collapse
Affiliation(s)
- Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Simone Bauer
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Petros Christopoulos
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
- Department of Oncology, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Anja Lisa Riediger
- Helmholtz Young Investigator Group, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Department of Urology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
| |
Collapse
|
|
21
|
Shao X, Wang H, Yu Y, Zhou C. Combined detection of stool-based methylation indicators for early screening of colorectal neoplasm. Am J Transl Res 2021; 13:11597-11607. [PMID: 34786085 PMCID: PMC8581910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
In the past two decades, several methylated DNA targets, including gene promoters and other intronic markers have been explored in tumors and benign lesions. Therefore, it can be expected that a panel of stool-based biomarkers will become a screening method for colorectal cancer (CRC) and adenoma with better sensitivity and specificity, aiming to decrease the incidence and mortality of CRC. In this study, the methylation of secreted frizzled-related protein 1 (SFRP1), hyperplastic polyposis protein 1 (HPP1), α-internexin (INA), Wnt inhibitory factor 1 (WIF1), tissue factor pathway inhibitor 2 (TFPI2), ikaros family zinc finger protein 1 (IKZF1), and spastic paraplegia 20 (SPG20) were detected in stool samples from patients with CRC, adenoma, polyps, and healthy controls, respectively, and these biomarkers were used to establish a logistic regression model for classification. Receiver operating characteristic (ROC) curves were drawn to assess the importance of each biomarker. Subsequently, a biomarker or combination of biomarkers was analyzed for early screening of high-risk neoplasm. The data showed that when a single biomarker was used for CRC screening, the sensitivity ranged from 63.9% to 76.8%, the area under the curve (AUC) ranged from 0.821 to 0.875, and the accuracy ranged from 77.0% to 84.5%. Finally, the methylation of SFRP1, HPP1, TFPI2, and IKZF1 was selected using a backward stepwise method in the multivariate logistic analysis according to the Akaike Information Criterion. These findings indicate that stool DNA biomarkers have good diagnostic power in discriminating high-risk level of neoplasm from healthy population.
Collapse
Affiliation(s)
- Xinyu Shao
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University Suzhou, Jiangsu, China
| | - Huiyu Wang
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University Suzhou, Jiangsu, China
| | - Yang Yu
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University Suzhou, Jiangsu, China
| | - Chunli Zhou
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University Suzhou, Jiangsu, China
| |
Collapse
|
|
22
|
Xu F, Yu S, Han J, Zong M, Tan Q, Zeng X, Fan L. Detection of Circulating Tumor DNA Methylation in Diagnosis of Colorectal Cancer. Clin Transl Gastroenterol 2021; 12:e00386. [PMID: 34382948 PMCID: PMC8367071 DOI: 10.14309/ctg.0000000000000386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Emerging evidence has demonstrated the potential of the circulating tumor DNA (ctDNA) methylation in the application of cancer diagnosis. METHODS Three genes including Septin9, Syndecan-2 (SDC2), and branched-chain amino acid transaminase 1 (BCAT1), which have been well demonstrated to have aberrant expression in colorectal cancer (CRC) as tumor suppressors, were selected for detection. A total of 234 peripheral plasma samples from 104 patients with CRC and 130 patients with colorectal polyps, and 60 plasma samples from healthy controls, were collected before any treatment. A real-time polymerase chain reaction-based gene panel was used to detect the methylation of Septin9, SDC2, and BCAT1. The composite score (P) was calculated according to the cycle threshold values of the 3 methylated genes using the logistic regression equation. RESULTS The ctDNA methylation of the 3 genes had a significantly higher level in patients with CRC, compared with patients with colorectal polyps and healthy controls. The composite score (P) showed association with tumor stages in CRC but not with the tumor location (colon or rectum). In addition, BCAT1 and Septin9 showed better performance for CRC diagnosis, by which CRC was able to distinguish from polyps with sensitivity of 83.7%, specificity of 93.9%, and area under the curve of 0.908. The diagnostic efficiency was significantly improved by combining composite score (P), carcinoembryonic antigen, and fecal immunochemical test for hemoglobin (area under the curve = 0.962). DISCUSSION The composite score (P) derived from the ctDNA methylation levels of Septin9, SDC2, and BCAT1 can be used for CRC diagnosis with high sensitivity and high specificity. A combination of ctDNA methylation, carcinoembryonic antigen, and fecal immunochemical test for hemoglobin was proved to be the most effective approach to diagnose CRC.
Collapse
Affiliation(s)
- Fei Xu
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, P. R. China;
| | - Shanshan Yu
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, P. R. China;
| | - Junyi Han
- Department of Gastrointestinal and Colorectal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Ming Zong
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, P. R. China;
| | - Qi Tan
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, P. R. China;
| | - Xin Zeng
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, P. R. China;
| | - Lieying Fan
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, P. R. China;
| |
Collapse
|
|
23
|
El Kadmiri N. Advances in Early Detection of Colorectal Cancer: A Focus on Non-invasive Biomarkers. Curr Drug Targets 2021; 22:1043-1053. [PMID: 33655856 DOI: 10.2174/1389450122666210303100048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/09/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide. Currently, colonoscopy remains the gold standard diagnostic test for CRC detection. Nonetheless, this technique is invasive and expensive. Remarkable ongoing strategies are focusing on the development of affordable methods to diagnose CRC at earlier stages. The introduction of suitable noninvasive, sensitive and specified diagnostic tests for early CRC detection by employing biomarker analysis seems to be a fundamental need to reduce the numbers of unnecessary colonoscopies. In this review, we provide an overview of single- and multi-panel biomarkers (Genomic markers, transcriptome markers, proteomic markers, inflammatory markers, and microbiome markers) encompassing noninvasive tests in blood and stool for early CRC detection. METHODS A bibliographic search using PubMed/Medline, Web of Science, and EBSCOhost databases was performed to find relevant published studies over the last 6 years. Forty-three pertinent studies were included in this review. RESULTS The primary outcome highlights the sensitivity and specificity of single diagnostic biomarkers studied in blood or stool. The secondary outcome reveals the sensitivity and specificity of the biomarkers panel (combinations) in blood or stool. While some markers show better performance, others are not suitable for screening purposes. CONCLUSION There is a need to adjust experimental and analytical tests that can interfere with a robust result to replace or supplement those markers that are currently in use. Nevertheless, robust verification and validation with large clinical cohorts are needed for successful noninvasive tests that can fulfill the role of colonoscopy.
Collapse
Affiliation(s)
- Nadia El Kadmiri
- Molecular Engineering, Valorization and Environment Team, Polydisciplinary Faculty of Taroudant, IBN ZOHR University, Taroudannt, Morocco
| |
Collapse
|
|
24
|
Young GP, Chen G, Wilson CJ, McGrane E, Hughes-Barton DLA, Flight IHK, Symonds EL. "Rescue" of Nonparticipants in Colorectal Cancer Screening: A Randomized Controlled Trial of Three Noninvasive Test Options. Cancer Prev Res (Phila) 2021; 14:803-810. [PMID: 34127509 DOI: 10.1158/1940-6207.capr-21-0080] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/07/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022]
Abstract
Few studies have directly targeted nonparticipants in colorectal cancer screening to identify effective engagement strategies. We undertook a randomized controlled trial that targeted nonparticipants in a previous trial of average-risk subjects which compared participation rates for mailed invitations offering a fecal test, a blood test or a choice of either. Nonparticipants (n = 899) were randomized to be offered a kit containing a fecal immunochemical test (FIT), directions on how to arrange a blood DNA test, or the option of doing either. Screening participation was assessed 12 weeks after the offer. To assess the cognitive and attitudinal variables related to participation and invitee choice, invitees were surveyed after 12 weeks, and associations were investigated using multinomial logistic regression. Participation rates were similar between groups (P = 0.88): 12.0% for FIT (35/292), 13.3% for the blood test (39/293), and 13.4% for choice (39/290). Within the choice group, participation was significantly higher with FIT (9.7%, 28/290) compared with the blood test (3.8%, 11/290, P = 0.005). The only variable significantly associated with participation was socioeconomic status when offered FIT, and age when offered choice but there was none when offered the blood test. Survey respondents indicated that convenience, time-saving, comfort, and familiarity were major influences on participation. There was no clear advantage between a fecal test, blood test, or choice of test although, when given a choice, the fecal test was preferred. Differences in variables associated with participation according to invitation strategy warrant consideration when deciding upon an invitation strategy for screening nonparticipants. PREVENTION RELEVANCE: This trial of screening for those at average risk for colorectal cancer targeted past fecal-test nonparticipants and compared participation rates for mailed invitations offering a fecal test, blood test, or choice of either. Although there was no clear advantage between strategies, factors associated with participation differed between each strategy.
Collapse
Affiliation(s)
- Graeme Paul Young
- Flinders Centre for Innovation in Cancer, Flinders Medical Centre, Bedford Park, South Australia, Australia. .,Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Gang Chen
- Centre for Health Economics, Monash University, Caufield East, Victoria, Australia
| | - Carlene J Wilson
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia.,School of Psychology and Public Health, LaTrobe University, Bundoora, Victoria, Australia
| | - Ellen McGrane
- School of Health and Related Research, University of Sheffield, Sheffield, United Kingdom
| | - Donna Lee-Ann Hughes-Barton
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Ingrid Helen K Flight
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Erin Leigh Symonds
- Flinders Centre for Innovation in Cancer, Flinders Medical Centre, Bedford Park, South Australia, Australia.,Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia.,Bowel Health Service, Flinders Medical Centre, Bedford Park, South Australia, Australia
| |
Collapse
|
|
25
|
Nassar FJ, Msheik ZS, Nasr RR, Temraz SN. Methylated circulating tumor DNA as a biomarker for colorectal cancer diagnosis, prognosis, and prediction. Clin Epigenetics 2021; 13:111. [PMID: 34001239 PMCID: PMC8130320 DOI: 10.1186/s13148-021-01095-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022] Open
Abstract
Worldwide, colorectal cancer (CRC) is a deadly disease whose death rate ranks second among cancers though its incidence ranks third. Early CRC detection is key and is associated with improved survival outcomes. However, existing tests for CRC diagnosis have several weaknesses thus rendering them inefficient. Moreover, reliable prognostic tests that can predict the overall cancer outcome and recurrence of the disease as well as predictive markers that can assess effectiveness of therapy are still lacking. Thus, shifting to noninvasive liquid biopsy or blood-based biomarkers is vital to improving CRC diagnosis, prognosis, and prediction. Methylated circulating tumor DNA (ctDNA) has gained increased attention as a type of liquid biopsy that is tumor-derived fragmented DNA with epigenetic alterations. Methylated ctDNA are more consistently present in blood of cancer patients as compared to mutated ctDNA. Hence, methylated ctDNA serves as a potential biomarker for CRC that is worth investigating. In this review, we explore what has been reported about methylated ctDNA as a biomarker for CRC diagnosis that can distinguish between CRC patients or those having adenoma and healthy controls as validated specifically through ROC curves. We also examine methylated ctDNA as a biomarker for CRC prognosis and prediction as confirmed through robust statistical analyses. Finally, we discuss the major technical challenges that limits the use of methylated ctDNA for clinical application and suggest possible recommendations to enhance its usage.
Collapse
Affiliation(s)
- Farah J Nassar
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon
| | - Zahraa S Msheik
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon
| | - Rihab R Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon.
| | - Sally N Temraz
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon.
| |
Collapse
|
|
26
|
Morris VK, Strickler JH. Use of Circulating Cell-Free DNA to Guide Precision Medicine in Patients with Colorectal Cancer. Annu Rev Med 2021; 72:399-413. [PMID: 33502901 DOI: 10.1146/annurev-med-070119-120448] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Patient-specific biomarkers form the foundation of precision medicine strategies. To realize the promise of precision medicine in patients with colorectal cancer (CRC), access to cost-effective, convenient, and safe assays is critical. Improvements in diagnostic technology have enabled ultrasensitive and specific assays to identify cell-free DNA (cfDNA) from a routine blood draw. Clinicians are already employing these minimally invasive assays to identify drivers of therapeutic resistance and measure genomic heterogeneity, particularly when tumor tissue is difficult to access or serial sampling is necessary. As cfDNA diagnostic technology continues to improve, more innovative applications are anticipated. In this review, we focus on four clinical applications for cfDNA analysis in the management of CRC: detecting minimal residual disease, monitoring treatment response in the metastatic setting, identifying drivers of treatment sensitivity and resistance, and guiding therapeutic strategies to overcome resistance.
Collapse
Affiliation(s)
- Van K Morris
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - John H Strickler
- Division of Medical Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| |
Collapse
|
|
27
|
Farooq M, Herman JG. Noninvasive Diagnostics for Early Detection of Lung Cancer: Challenges and Potential with a Focus on Changes in DNA Methylation. Cancer Epidemiol Biomarkers Prev 2020; 29:2416-2422. [PMID: 33148791 PMCID: PMC11559093 DOI: 10.1158/1055-9965.epi-20-0704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/20/2020] [Accepted: 10/13/2020] [Indexed: 11/16/2022] Open
Abstract
Lung cancer remains the leading cause of cancer deaths in the United States and the world. Early detection of this disease can reduce mortality, as demonstrated for low-dose computed tomography (LDCT) screening. However, there remains a need for improvements in lung cancer detection to complement LDCT screening and to increase adoption of screening. Molecular changes in the tumor, and the patient's response to the presence of the tumor, have been examined as potential biomarkers for diagnosing lung cancer. There are significant challenges to developing an effective biomarker with sufficient sensitivity and specificity for the early detection of lung cancer, particularly the detection of circulating tumor DNA, which is present in very small quantities. We will review approaches to develop biomarkers for the early detection of lung cancer, with special consideration to detection of rare tumor events, focus on the use of DNA methylation-based detection in plasma and sputum, and discuss the promise and challenges of lung cancer early detection. Plasma-based detection of lung cancer DNA methylation may provide a simple cost-effective method for the early detection of lung cancer.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
Collapse
Affiliation(s)
- Maria Farooq
- Department of Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - James G Herman
- Department of Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
- UPMC Hillman Comprehensive Cancer Center, Pittsburgh, Pennsylvania
| |
Collapse
|
|
28
|
Li QX, Li NQ, Liao JY. Diagnostic and prognostic values of forkhead box D4 gene in colonic adenocarcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:2615-2627. [PMID: 33165349 PMCID: PMC7642708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Previous studies found that Forkhead box D4 (FOXD4) overexpressed in human colorectal cancer had the worst prognosis. However, the diagnostic value and further mechanism have not been fully researched. Statistical examinations for FOXD4 expression colon adenocarcinoma (COAD) patients were obtained from The Cancer Genome Atlas (TCGA). Survival analysis was used to assess its prognostic value. Nomogram model was used for visual prediction of patient survival rate. The online functional enrichment analysis tool was used to evaluate the biological functions and pathways of FOXD4 and its co-expressed genes. Receiver operating characteristic curve analysis suggested that FOXD4 might be a diagnostic biomarker for COAD (P<0.001, area under the curve [AUC]=0.728, 95% confidence interval [CI]=0.669-0.787). Low expression of FOXD4 was associated with a good clinical outcome (P=0.001, HR=0.517, 95% CI=0.341-0.782). A total of 797 genes were correlated with FOXD4 and associated with cell proliferation, cell differentiation, nuclear matrix, Rap1 signaling pathway, RNA transport, and VEGF signaling pathway. In conclusion, expression of FOXD4 may be a diagnostic and prognostic biomarker in COAD.
Collapse
Affiliation(s)
- Qiu-Xia Li
- Department of Health Management and Division of Physical Examination, The First Affiliated Hospital of Guangxi Medical UniversityNanning 530021, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Ning-Qin Li
- Department of Radiology, The First Affiliated Hospital of Guangxi Medical UniversityNanning 530021, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Jin-Yuan Liao
- Department of Radiology, The First Affiliated Hospital of Guangxi Medical UniversityNanning 530021, Guangxi Zhuang Autonomous Region, People’s Republic of China
| |
Collapse
|
|
29
|
Musher BL, Melson JE, Amato G, Chan D, Hill M, Khan I, Kochuparambil ST, Lyons SE, Orsini J, Pedersen SK, Robb B, Saltzman J, Silinsky J, Gaur S, Tuck MK, LaPointe LC, Young GP. Evaluation of Circulating Tumor DNA for Methylated BCAT1 and IKZF1 to Detect Recurrence of Stage II/Stage III Colorectal Cancer (CRC). Cancer Epidemiol Biomarkers Prev 2020; 29:2702-2709. [DOI: 10.1158/1055-9965.epi-20-0574] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/27/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022] Open
|
|
30
|
Hideura E, Suehiro Y, Nishikawa J, Shuto T, Fujimura H, Ito S, Goto A, Hamabe K, Saeki I, Okamoto T, Higaki S, Fujii I, Suzuki C, Hoshida T, Matsumoto T, Takami T, Sakaida I, Yamasaki T. Blood Free-Circulating DNA Testing of Methylated RUNX3 Is Useful for Diagnosing Early Gastric Cancer. Cancers (Basel) 2020; 12:cancers12040789. [PMID: 32224873 PMCID: PMC7226141 DOI: 10.3390/cancers12040789] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/24/2022] Open
Abstract
The main modalities for gastric cancer screening are limited to upper gastrointestinal endoscopy and contrast radiography. The former is invasive, and the latter has high false-negative rates. Thus, alternative diagnostic strategies are required. One solution may be a liquid biopsy. Methylated RUNX3 is a well-known biomarker of gastric cancer but it is very difficult to detect with conventional bisulfite-based methylation assays when only a small amount of serum is available. We developed the combined restriction digital PCR (CORD) assay, a new methylation assay allowing for the counting of as little as one copy of a methylated gene in a small sample of DNA without necessitating DNA bisulfite treatment. We evaluated the sensitivity and specificity of the serum DNA testing of methylated RUNX3 by the CORD assay for the detection of early gastric cancer using 50 patients with early gastric cancer and 61 control individuals. The CORD assay had a sensitivity of 50.0% and a specificity of 80.3% for early gastric cancer. Methylated RUNX3 copies were significantly associated with tumor size, massive submucosal invasion, and lymph-vascular invasion. After the treatment, the median number of methylated RUNX3 copies was significantly decreased. The CORD assay may provide an alternative screening strategy to detect even early-stage gastric cancer.
Collapse
Affiliation(s)
- Eizaburou Hideura
- Department of Gastroenterology and Hepatology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (E.H.); (H.F.); (S.I.); (A.G.); (K.H.); (I.S.); (T.O.); (T.T.); (I.S.)
| | - Yutaka Suehiro
- Department of Oncology and Laboratory Medicine, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (T.H.); (T.M.); (T.Y.)
- Correspondence: (Y.S.); (J.N.); Tel.: +81-836-22-2337 (Y.S.); Fax: +81-836-22-2338 (Y.S.); Tel./Fax: +81-836-22-2835 (J.N.)
| | - Jun Nishikawa
- Faculty of Laboratory Science, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan;
- Correspondence: (Y.S.); (J.N.); Tel.: +81-836-22-2337 (Y.S.); Fax: +81-836-22-2338 (Y.S.); Tel./Fax: +81-836-22-2835 (J.N.)
| | - Takuya Shuto
- Faculty of Laboratory Science, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan;
| | - Hiroyuki Fujimura
- Department of Gastroenterology and Hepatology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (E.H.); (H.F.); (S.I.); (A.G.); (K.H.); (I.S.); (T.O.); (T.T.); (I.S.)
| | - Shunsuke Ito
- Department of Gastroenterology and Hepatology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (E.H.); (H.F.); (S.I.); (A.G.); (K.H.); (I.S.); (T.O.); (T.T.); (I.S.)
| | - Atsushi Goto
- Department of Gastroenterology and Hepatology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (E.H.); (H.F.); (S.I.); (A.G.); (K.H.); (I.S.); (T.O.); (T.T.); (I.S.)
| | - Kouichi Hamabe
- Department of Gastroenterology and Hepatology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (E.H.); (H.F.); (S.I.); (A.G.); (K.H.); (I.S.); (T.O.); (T.T.); (I.S.)
| | - Issei Saeki
- Department of Gastroenterology and Hepatology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (E.H.); (H.F.); (S.I.); (A.G.); (K.H.); (I.S.); (T.O.); (T.T.); (I.S.)
| | - Takeshi Okamoto
- Department of Gastroenterology and Hepatology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (E.H.); (H.F.); (S.I.); (A.G.); (K.H.); (I.S.); (T.O.); (T.T.); (I.S.)
| | - Shingo Higaki
- Department of Gastroenterology, St. Hill Hospital, Ube 755-8505, Japan;
| | - Ikuei Fujii
- Ajisu Kyoritsu Hospital, Yamaguchi 754-1277, Japan; (I.F.); (C.S.)
| | - Chieko Suzuki
- Ajisu Kyoritsu Hospital, Yamaguchi 754-1277, Japan; (I.F.); (C.S.)
| | - Tomomi Hoshida
- Department of Oncology and Laboratory Medicine, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (T.H.); (T.M.); (T.Y.)
| | - Toshihiko Matsumoto
- Department of Oncology and Laboratory Medicine, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (T.H.); (T.M.); (T.Y.)
| | - Taro Takami
- Department of Gastroenterology and Hepatology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (E.H.); (H.F.); (S.I.); (A.G.); (K.H.); (I.S.); (T.O.); (T.T.); (I.S.)
| | - Isao Sakaida
- Department of Gastroenterology and Hepatology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (E.H.); (H.F.); (S.I.); (A.G.); (K.H.); (I.S.); (T.O.); (T.T.); (I.S.)
| | - Takahiro Yamasaki
- Department of Oncology and Laboratory Medicine, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; (T.H.); (T.M.); (T.Y.)
| |
Collapse
|
|
31
|
Constâncio V, Nunes SP, Henrique R, Jerónimo C. DNA Methylation-Based Testing in Liquid Biopsies as Detection and Prognostic Biomarkers for the Four Major Cancer Types. Cells 2020; 9:E624. [PMID: 32150897 PMCID: PMC7140532 DOI: 10.3390/cells9030624] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022] Open
Abstract
Lung, breast, colorectal, and prostate cancers are the most incident worldwide. Optimal population-based cancer screening methods remain an unmet need, since cancer detection at early stages increases the prospects of successful and curative treatment, leading to a lower incidence of recurrences. Moreover, the current parameters for cancer patients' stratification have been associated with divergent outcomes. Therefore, new biomarkers that could aid in cancer detection and prognosis, preferably detected by minimally invasive methods are of major importance. Aberrant DNA methylation is an early event in cancer development and may be detected in circulating cell-free DNA (ccfDNA), constituting a valuable cancer biomarker. Furthermore, DNA methylation is a stable alteration that can be easily and rapidly quantified by methylation-specific PCR methods. Thus, the main goal of this review is to provide an overview of the most important studies that report methylation biomarkers for the detection and prognosis of the four major cancers after a critical analysis of the available literature. DNA methylation-based biomarkers show promise for cancer detection and management, with some studies describing a "PanCancer" detection approach for the simultaneous detection of several cancer types. Nonetheless, DNA methylation biomarkers still lack large-scale validation, precluding implementation in clinical practice.
Collapse
Affiliation(s)
- Vera Constâncio
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Sandra P. Nunes
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
| | - Rui Henrique
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| |
Collapse
|
|
32
|
Locke WJ, Guanzon D, Ma C, Liew YJ, Duesing KR, Fung KYC, Ross JP. DNA Methylation Cancer Biomarkers: Translation to the Clinic. Front Genet 2019; 10:1150. [PMID: 31803237 PMCID: PMC6870840 DOI: 10.3389/fgene.2019.01150] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022] Open
Abstract
Carcinogenesis is accompanied by widespread DNA methylation changes within the cell. These changes are characterized by a globally hypomethylated genome with focal hypermethylation of numerous 5’-cytosine-phosphate-guanine-3’ (CpG) islands, often spanning gene promoters and first exons. Many of these epigenetic changes occur early in tumorigenesis and are highly pervasive across a tumor type. This allows DNA methylation cancer biomarkers to be suitable for early detection and also to have utility across a range of areas relevant to cancer detection and treatment. Such tests are also simple in construction, as only one or a few loci need to be targeted for good test coverage. These properties make cancer-associated DNA methylation changes very attractive for development of cancer biomarker tests with substantive clinical utility. Across the patient journey from initial detection, to treatment and then monitoring, there are several points where DNA methylation assays can inform clinical practice. Assays on surgically removed tumor tissue are useful to determine indicators of treatment resistance, prognostication of outcome, or to molecularly characterize, classify, and determine the tissue of origin of a tumor. Cancer-associated DNA methylation changes can also be detected with accuracy in the cell-free DNA present in blood, stool, urine, and other biosamples. Such tests hold great promise for the development of simple, economical, and highly specific cancer detection tests suitable for population-wide screening, with several successfully translated examples already. The ability of circulating tumor DNA liquid biopsy assays to monitor cancer in situ also allows for the ability to monitor response to therapy, to detect minimal residual disease and as an early biomarker for cancer recurrence. This review will summarize existing DNA methylation cancer biomarkers used in clinical practice across the application domains above, discuss what makes a suitable DNA methylation cancer biomarker, and identify barriers to translation. We discuss technical factors such as the analytical performance and product-market fit, factors that contribute to successful downstream investment, including geography, and how this impacts intellectual property, regulatory hurdles, and the future of the marketplace and healthcare system.
Collapse
Affiliation(s)
- Warwick J Locke
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Dominic Guanzon
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Chenkai Ma
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia
| | - Yi Jin Liew
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Konsta R Duesing
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia
| | - Kim Y C Fung
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Jason P Ross
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| |
Collapse
|
|
33
|
Danese E, Montagnana M, Lippi G. Circulating molecular biomarkers for screening or early diagnosis of colorectal cancer: which is ready for prime time? ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:610. [PMID: 32047771 PMCID: PMC7011594 DOI: 10.21037/atm.2019.08.97] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022]
Abstract
According to recent statistics, colorectal cancer (CRC) is a frequent disease, the second most frequent malignancy in women and the third most common malignant disease in men, respectively. Although reinforced emphasis on CRC screening by means of immunochemical fecal occult blood test, colonoscopy or sigmoidoscopy has contributed to decrease cancer-related deaths, alternative diagnostic tests would be needed for establishing earlier and more potentially effective treatments. Innovative diagnostic techniques have recently emerged, some of which hold promises for screening and/or early CRC detection. Recent evidence suggests that the so-called "liquid biopsy", conventionally defined as detection and quantification of circulating tumor cells (CTCs) and cancer-related nucleic acids in peripheral blood, may allow earlier diagnosis of CRC combined with lower invasiveness and less patient inconvenience, higher throughput, faster turnaround time, inferior usage of healthcare resources and relatively low cost. Encouraging data have emerged from trials based on CTCs detection, though the sensitivity of the current diagnostic techniques is still perhaps insufficient for enabling early CRC diagnosis. Among the various biomarkers that can be detected with liquid biopsy, SEPT9 methylation displays good diagnostic performance and relatively high cancer detection rate (between 57-64% in patients with CRC stages 0-I), which would make this test a promising tool for population screening, alone or in combination with other conventional diagnostic investigations. Encouraging evidence has also been recently published for BCAT1/IKZF1 methylation. Regarding microRNA (miRNAs), the available evidence highlights that the combination of some of these biomarkers rather than the assessment of a single miRNA alone would enable efficient identification of early CRCs, though widespread clinical application is still challenged by a number of preanalytical, analytical and clinical issues.
Collapse
Affiliation(s)
- Elisa Danese
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | | | - Giuseppe Lippi
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| |
Collapse
|
|
34
|
Zhan YX, Luo GH. DNA methylation detection methods used in colorectal cancer. World J Clin Cases 2019; 7:2916-2929. [PMID: 31624740 PMCID: PMC6795732 DOI: 10.12998/wjcc.v7.i19.2916] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/22/2019] [Accepted: 09/09/2019] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) remains a major contributor to the number of cancer-related deaths that occur annually worldwide. With the development of molecular biology methods, an increasing number of molecular biomarkers have been identified and investigated. CRC is believed to result from an accumulation of epigenetic changes, and detecting aberrant DNA methylation patterns is useful for both the early diagnosis and prognosis of CRC. Numerous studies are focusing on the development of DNA methylation detection methods or DNA methylation panels. Thus, this review will discuss the commonly used techniques and technologies to evaluate DNA methylation, their merits and deficiencies as well as the prospects for new methods.
Collapse
Affiliation(s)
- Yu-Xia Zhan
- Comprehensive Laboratory, Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research, the Third Affiliated Hospital of Soochow University, Changzhou 213003, Jiangsu Province, China
| | - Guang-Hua Luo
- Comprehensive Laboratory, Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research, the Third Affiliated Hospital of Soochow University, Changzhou 213003, Jiangsu Province, China
| |
Collapse
|
|
35
|
Low Sensitivity of Fecal Immunochemical Tests and Blood-Based Markers of DNA Hypermethylation for Detection of Sessile Serrated Adenomas/Polyps. Dig Dis Sci 2019; 64:2555-2562. [PMID: 30835026 DOI: 10.1007/s10620-019-05569-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 02/26/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Early detection and removal of precursor lesions reduce colorectal cancer morbidity and mortality. Sessile serrated adenomas/polyps (SSP) are a recognized precursor of cancer, but there are limited studies on whether current screening techniques detect this pathology. AIMS To investigate the sensitivity of fecal immunochemical tests (FIT) and epigenetic biomarkers in blood for detection of SSP. METHODS A prospective study offered FIT and a blood test (Colvera for methylated BCAT1 and IKZF1) to adults referred for colonoscopy. Sensitivity of FIT and the blood test were determined for four types of pathology: low-risk conventional adenoma, high-risk adenoma, SSP, and absence of neoplasia. Comparisons were made for FIT positivity at 10 and 20 μg hemoglobin (Hb)/g feces. RESULTS One thousand eight hundred and eighty-two subjects completed FIT and underwent colonoscopy. One thousand four hundred and three were also tested for methylated BCAT1/IKZF1. The sensitivity of FIT (20 μg Hb/g feces) for SSP was 16.3%. This was lower than the sensitivity for high-risk adenomas (28.7%, p < 0.05), but no different to that for low-risk adenomas (13.1%) or no neoplasia (8.4%). A positive FIT result for SSP was not associated with demographics, morphology, concurrent pathology or intake of medications that increase bleeding risk. FIT sensitivity for SSP did not significantly increase through lowering the positivity threshold to 10 μg Hb/g feces (20.4%, p > 0.05). Sensitivity of the blood test for SSP was 8.8%, and 26.5% when combined with FIT. CONCLUSIONS Both FIT and blood-based markers of DNA hypermethylation have low sensitivity for detection of SSP. Further development of sensitive screening tests is warranted.
Collapse
|
|
36
|
Symonds EL, Hughes D, Flight I, Woodman R, Chen G, Ratcliffe J, Pedersen SK, Fraser RJL, Wilson CJ, Young GP. A Randomized Controlled Trial Testing Provision of Fecal and Blood Test Options on Participation for Colorectal Cancer Screening. Cancer Prev Res (Phila) 2019; 12:631-640. [PMID: 31266825 DOI: 10.1158/1940-6207.capr-19-0089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/24/2019] [Accepted: 06/27/2019] [Indexed: 11/16/2022]
Abstract
Suboptimal participation is commonly observed in colorectal cancer screening programs utilizing fecal tests. This randomized controlled trial tested whether the offer of a blood test as either a "rescue" strategy for fecal test nonparticipants or an upfront choice, could improve participation. A total of 1,800 people (50-74 years) were randomized to control, rescue, or choice groups (n = 600/group). All were mailed a fecal immunochemical test (FIT, OC-Sensor, Eiken Chemical Company) and a survey assessing awareness of the screening tests. The rescue group was offered a blood test 12 weeks after FIT nonparticipation. The choice group was given the opportunity to choose to do a blood test (Colvera, Clinical Genomics) instead of FIT at baseline. Participation with any test after 24 weeks was not significantly different between groups (control, 37.8%; rescue, 36.9%; choice, 33.8%; P > 0.05). When the rescue strategy was offered after 12 weeks, an additional 6.5% participated with the blood test, which was greater than the blood test participation when offered as an upfront choice (1.5%; P < 0.001). Awareness of the tests was greater for FIT than for blood (96.2% vs. 23.1%; P < 0.0001). In a population familiar with FIT screening, provision of a blood test either as a rescue of FIT nonparticipants or as an upfront choice did not increase overall participation. This might reflect a lack of awareness of the blood test for screening compared with FIT.
Collapse
Affiliation(s)
- Erin L Symonds
- Flinders Centre for Innovation in Cancer, Bedford Park, South Australia, Australia. .,Bowel Health Service, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Donna Hughes
- Flinders Centre for Innovation in Cancer, Bedford Park, South Australia, Australia
| | - Ingrid Flight
- Flinders Centre for Innovation in Cancer, Bedford Park, South Australia, Australia
| | - Richard Woodman
- Flinders Centre for Epidemiology and Biostatistics, School of Medicine, Flinders University, Bedford Park, South Australia, Australia
| | - Gang Chen
- Centre for Health Economics, Monash University, Caulfield East, Victoria, Australia
| | - Julie Ratcliffe
- College of Nursing and Health Sciences, Health and Social Care Economics Group, Flinders University, Bedford Park, South Australia, Australia
| | | | - Robert J L Fraser
- Flinders Centre for Innovation in Cancer, Bedford Park, South Australia, Australia.,Department of Gastroenterology and Hepatology, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Carlene J Wilson
- Flinders Centre for Innovation in Cancer, Bedford Park, South Australia, Australia.,School of Psychology & Public Health, La Trobe University, Bundoora, Victoria, Australia
| | - Graeme P Young
- Flinders Centre for Innovation in Cancer, Bedford Park, South Australia, Australia
| |
Collapse
|
|
37
|
Cell-Free DNA as a Diagnostic Blood-Based Biomarker for Colorectal Cancer: A Systematic Review. J Surg Res 2019; 236:184-197. [PMID: 30694754 DOI: 10.1016/j.jss.2018.11.029] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/18/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023]
|
|
38
|
Murray DH, Symonds EL, Young GP, Byrne S, Rabbitt P, Roy A, Cornthwaite K, Karapetis CS, Pedersen SK. Relationship between post-surgery detection of methylated circulating tumor DNA with risk of residual disease and recurrence-free survival. J Cancer Res Clin Oncol 2018; 144:1741-1750. [PMID: 29992492 DOI: 10.1007/s00432-018-2701-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/03/2018] [Indexed: 02/06/2023]
Abstract
PURPOSE Methylation in IKZF1 and BCAT1 are common events in colorectal cancer (CRC). They are often detected in blood as circulating tumor DNA (ctDNA) at diagnosis and disappear after surgery in most CRC patients. A prospective study was conducted to determine the relationship between detection of these markers following surgery and risk for residual disease and for recurrence. METHODS ctDNA status with methylated BCAT1 and IKZF1 was determined within 12 months of surgical resection of CRC, and was related to presence of or risk for residual disease (margins involved, metastases present or nature of node involvement), and to recurrence-free survival. RESULTS Blood was collected from 172 CRC patients after surgery and 28 (16%) were ctDNA positive. Recurrence was diagnosed in 23 of the 138 with clinical follow-up after surgery (median follow-up 23.3 months, IQR 14.3-29.5). Multivariate modeling indicated that features suggestive of residual disease were an independent predictor of post-surgery ctDNA status: cases with any of three features (close resection margins, apical node involved, or distant metastases) were 5.3 times (95% CI 1.5-18.4, p = 0.008) more likely to be ctDNA positive. Multivariate analysis showed that post-surgery ctDNA positivity was independently associated with an increased risk of recurrence (HR 3.8, 1.5-9.5, p = 0.004). CONCLUSIONS CRC cases positive for methylated ctDNA after surgery are at increased risk of residual disease and subsequently recurrence. This could have implications for guiding recommendations for adjuvant therapy and surveillance strategies. Randomized studies are now indicated to determine if monitoring cases with these biomarkers leads to survival benefit.
Collapse
Affiliation(s)
| | - Erin L Symonds
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, SA, 5042, Australia.
- Bowel Health Service, Flinders Medical Centre, Bedford Park, SA, Australia.
| | - Graeme P Young
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, SA, 5042, Australia
| | - Susan Byrne
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, SA, 5042, Australia
| | - Philippa Rabbitt
- Colorectal Surgery, Division of Surgery and Perioperative Medicine, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Amitesh Roy
- Department of Oncology, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Kathryn Cornthwaite
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, SA, 5042, Australia
| | | | | |
Collapse
|
|
39
|
Oliveira IBDD, Hirata RDC. Circulating cell-free DNA as a biomarker in the diagnosis and prognosis of colorectal cancer. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902018000117368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
|
|
40
|
Symonds EL, Pedersen SK, Murray DH, Jedi M, Byrne SE, Rabbitt P, Baker RT, Bastin D, Young GP. Circulating tumour DNA for monitoring colorectal cancer-a prospective cohort study to assess relationship to tissue methylation, cancer characteristics and surgical resection. Clin Epigenetics 2018; 10:63. [PMID: 29796114 PMCID: PMC5956533 DOI: 10.1186/s13148-018-0500-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/10/2018] [Indexed: 12/19/2022] Open
Abstract
Background Cell-free circulating tumour-derived DNA (ctDNA) can be detected by testing for methylated BCAT1 and IKZF1 DNA, which has proven sensitivity for colorectal cancer (CRC). A prospective correlative biomarker study between presence of methylated BCAT1 and IKZF1 in tissue and blood was conducted in cases with CRC to explore how detection of such ctDNA biomarkers relates to cancer characteristics, methylation in tissue and surgical resection of the primary cancer. Methods Enrolled patients with invasive CRC had blood collected at diagnosis, prior to any treatment or surgery (peri-diagnostic sample). A subgroup of patients also had cancer and adjacent non-neoplastic tissue collected at surgical resection, as well as a second blood sample collected within 12 months of surgery (post-surgery sample). DNA was extracted from all samples and assayed for methylated BCAT1 and IKZF1 to determine the degree of methylation in tissue and the presence of ctDNA in blood. Results Of 187 cases providing peri-diagnostic blood samples, tissue was available in 91, and 93 provided at least one post-surgery blood sample for marker analysis. Significant methylation of either BCAT1 or IKZF1 was seen in 86/91 (94.5%) cancer tissues, with levels independent of stage and higher than that observed in adjacent non-neoplastic specimens (P < 0.001). ctDNA methylated in BCAT1 or IKZF1 was detected in 116 (62.0%) cases at diagnosis and was significantly more likely to be detected with later stage (P < 0.001) and distal tumour location (P = 0.004). Of the 91 patients who provided pre-and post-surgery blood samples, 47 patients were ctDNA-positive at diagnosis and 35 (74.5%) became negative after tumour resection. Conclusion This study has shown that BCAT1 and IKZF1 methylation are common events in CRC with almost all cancer tissues showing significant levels of methylation in the two genes. The presence of ctDNA in blood is stage-related and show rapid reversion to negative following surgical resection. Monitoring methylated BCAT1 and IKZF1 levels could therefore inform adequacy of surgical resection. Trial registration Australian New Zealand Clinical Trial Registry number 12611000318987. Registered 25 March 2011. Electronic supplementary material The online version of this article (10.1186/s13148-018-0500-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Erin L Symonds
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia.,2Bowel Health Service, Flinders Medical Centre, Bedford Park, South Australia Australia
| | | | - David H Murray
- Clinical Genomics Pty Ltd, North Ryde, New South Wales Australia
| | - Maher Jedi
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
| | - Susan E Byrne
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
| | - Philippa Rabbitt
- 4Colorectal Surgery, Division of Surgery and Perioperative Medicine, Flinders Medical Centre, Bedford Park, South Australia Australia
| | - Rohan T Baker
- Clinical Genomics Pty Ltd, North Ryde, New South Wales Australia
| | - Dawn Bastin
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
| | - Graeme P Young
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
| |
Collapse
|
|
41
|
Jedi M, Young GP, Pedersen SK, Symonds EL. Methylation and Gene Expression of BCAT1 and IKZF1 in Colorectal Cancer Tissues. CLINICAL MEDICINE INSIGHTS-ONCOLOGY 2018; 12:1179554918775064. [PMID: 29780264 PMCID: PMC5952276 DOI: 10.1177/1179554918775064] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 04/12/2018] [Indexed: 12/20/2022]
Abstract
The genes BCAT1 and IKZF1 are hypermethylated in colorectal cancer (CRC), but little is known about how this relates to gene expression. This study assessed the relationship between methylation and gene expression of BCAT1 and IKZF1 in CRC and adjacent non-neoplastic tissues. The tissues were obtained at surgery from 36 patients diagnosed with different stages of CRC (stage I n = 8, stage II n = 13, stage III n = 10, stage IV n = 5). Methylated BCAT1 and IKZF1 were detected in 92% and 72% CRC tissues, respectively, with levels independent of stage (P > .05). In contrast, only 31% and 3% of non-neoplastic tissues were methylated for BCAT1 and IKZF1, respectively (P < .001). The IKZF1 messenger RNA (mRNA) expression was significantly lower in the cancer tissues compared with that of non-neoplastic tissues, whereas the BCAT1 mRNA levels were similar. The latter may be due to the BCAT1 polymerase chain reaction assay detecting more than 1 mRNA transcript. Further studies are warranted to establish the role of the epigenetic silencing of IKZF1 in colorectal oncogenesis.
Collapse
Affiliation(s)
- Maher Jedi
- Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Graeme P Young
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, SA, Australia
| | | | - Erin L Symonds
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, SA, Australia.,Bowel Health Service, Flinders Medical Centre, Bedford Park, SA, Australia
| |
Collapse
|
|
42
|
Wong CC, Li W, Chan B, Yu J. Epigenomic biomarkers for prognostication and diagnosis of gastrointestinal cancers. Semin Cancer Biol 2018; 55:90-105. [PMID: 29665409 DOI: 10.1016/j.semcancer.2018.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
Abstract
Altered epigenetic regulation is central to many human diseases, including cancer. Over the past two decade, major advances have been made in our understanding of the role of epigenetic alterations in carcinogenesis, particularly for DNA methylation, histone modifications and non-coding RNAs. Aberrant hypermethylation of DNA at CpG islands is a well-established phenomenon that mediates transcriptional silencing of tumor suppressor genes, and it is an early event integral to gastrointestinal cancer development. As such, detection of aberrant DNA methylation is being developed as biomarkers for prognostic and diagnostic purposes in gastrointestinal cancers. Diverse tissue types are suitable for the analyses of methylated DNA, such as tumor tissues, blood, plasma, and stool, and some of these markers are already utilized in the clinical setting. Recent advances in the genome-wide epigenomic approaches are enabling the comprehensive mapping of the cancer methylome, thus providing new avenues for mining novel biomarkers for disease prognosis and diagnosis. Here, we review the current knowledge on DNA methylation biomarkers for the prognostication and non-invasive diagnosis of gastrointestinal cancers and highlight their clinical application.
Collapse
Affiliation(s)
- Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong.
| | - Weilin Li
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Surgery, The Chinese University of Hong Kong, Hong Kong
| | - Bertina Chan
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong.
| |
Collapse
|
|
43
|
Blood free-circulating DNA testing by highly sensitive methylation assay to diagnose colorectal neoplasias. Oncotarget 2018; 9:16974-16987. [PMID: 29682198 PMCID: PMC5908299 DOI: 10.18632/oncotarget.24768] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/27/2018] [Indexed: 12/18/2022] Open
Abstract
Although methylated TWIST1 is a biomarker of colorectal neoplasia, its detection from serum samples is very difficult by conventional bisulfite-based methylation assays. Therefore, we have developed a new methylation assay that enables counting of even one copy of a methylated gene in a small DNA sample amount without DNA bisulfite treatment. We performed this study to evaluate the sensitivity and specificity of serum DNA testing by the new methylation assay in combination with and without the fecal immunochemical test for hemoglobin for the detection of colorectal neoplasia. This study comprised 113 patients with colorectal neoplasia and 25 control individuals. For the new methylation assay, DNA was treated in two stages with methylation-sensitive restriction enzymes, followed by measurement of copy numbers of hTERT and methylated TWIST1 by multiplex droplet digital PCR. The fecal immunochemical test had a sensitivity of 8.0% for non-advanced adenoma, 24.3% for advanced adenoma, and 44.4% for colorectal cancer, and a specificity of 88.0%. The new assay had a sensitivity of 36.0% for non-advanced adenoma, 30.0% for advanced adenoma, and 44.4% for colorectal cancer, and a specificity of 92.0%. Combination of the both tests increased the sensitivity to 40.0%, 45.7%, and 72.2% for the detection of non-advanced adenoma, advanced adenoma, and colorectal cancer, respectively, and resulted in a specificity of 84.0%. Combination of both tests may provide an alternative screening strategy for colorectal neoplasia including potentially precancerous lesions and colorectal cancer.
Collapse
|
|
44
|
Worm Ørntoft MB. Review of Blood-Based Colorectal Cancer Screening: How Far Are Circulating Cell-Free DNA Methylation Markers From Clinical Implementation? Clin Colorectal Cancer 2018; 17:e415-e433. [PMID: 29678513 DOI: 10.1016/j.clcc.2018.02.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 02/21/2018] [Accepted: 02/26/2018] [Indexed: 12/16/2022]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer related deaths worldwide, and late stages (III-IV) in particular have low 5-year survival rates. Stage shifting by CRC screening programs has proven effective by decreasing morbidity and mortality and in many countries national CRC screening programs have been implemented. Currently, European, Asian, and American authorities recommend screening for CRC using fecal occult blood testing, sigmoidoscopy, or colonoscopy. Because these approaches all have weaknesses (eg, poor compliance, high costs, test invasiveness), much effort has been put into the development of alternative screening approaches, many of which are blood-based. Blood-based strategies especially present the advantages of minimally invasiveness compared to endoscopies and an expectantly higher compliance rate compared to stool-based tests. The last decades have seen many discovery studies identifying promising blood-based biomarkers of CRC; however, common to all of these markers is that their clinical usefulness remains evasive. At present only one blood-based CRC screening marker has been approved in the United States. The aim of this review is to discuss the development of blood-based cell-free DNA methylation marker candidates for CRC screening. On the basis of a methodical literature search, the past, present, and future of cell-free DNA screening markers for CRC are revised and discussed. Resource limitations and technical challenges related to sensitivity and specificity measurements keep many markers at bay. Possible solutions to these problems are offered to enable markers to benefit future screening participants.
Collapse
|
|
45
|
Osborne JM, Flight I, Wilson CJ, Chen G, Ratcliffe J, Young GP. The impact of sample type and procedural attributes on relative acceptability of different colorectal cancer screening regimens. Patient Prefer Adherence 2018; 12:1825-1836. [PMID: 30271126 PMCID: PMC6154741 DOI: 10.2147/ppa.s172143] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE In Australia and other countries, participation in colorectal cancer (CRC) screening using fecal occult blood testing is low. Previous research suggests that fecal sampling induces disgust, so approaches not involving feces may increase participation. This study aimed to determine population preferences for CRC screening tests that utilize different sample collections (stool, blood, and saliva) and the extent to which specific attributes (convenience, performance, and cost) impact this preference. MATERIALS AND METHODS People aged 50-74 years completed a survey. Preference for screening for CRC through stool, blood, and saliva was judged through ranking of preference and attributes critical to preference and confirmed via a discrete choice experiment (DCE) where test attributes were described as varying by performance, cost, and sample type. Participants also completed a measure of aversion to sample type. RESULTS A total of 1,282 people participated in the survey. The DCE and ranking exercise confirmed that all test attributes had a statistically significant impact on respondents' preferences (P < 0.001). Blood and saliva were equally preferred over stool; however, test performance was the most influential attribute. In multivariable analyses, those who preferred blood to stool collection exhibited higher aversion to fecal (OR = 1.17; P ≤ 0.001) and saliva (OR = 1.06; P ≤ 0.05) sampling and perceived that they had less time for home sample collection (OR = 0.72, P ≤ 0.001). Those who preferred saliva to stool had higher aversion to fecal (OR = 1.15; P ≤ 0.001) and blood (OR = 1.06, P ≤ 0.01) sampling and less time for home sample collection (OR = 0.81, P ≤ 0.5). CONCLUSION Aversion to sample type and perceived inconvenience of sample collection are significant drivers of screening preference. While blood and saliva sampling were the most preferred methods, test performance was the most important attribute of a screening test, regardless of sample type. Efforts to increase CRC screening participation should focus on a test, or combination of tests, that combines the attributes of high performance, low aversion, and convenience of use.
Collapse
Affiliation(s)
- Joanne M Osborne
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, SA, Australia,
- Bowel Health Service, Repatriation General Hospital, Daw Park, SA, Australia
| | - Ingrid Flight
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, SA, Australia,
| | - Carlene J Wilson
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, SA, Australia,
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC, Australia,
- Olivia Newton John Cancer Wellness and Research Centre, Austin Hospital, Heidelberg, VIC, Australia,
| | - Gang Chen
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, SA, Australia,
| | - Julie Ratcliffe
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, SA, Australia,
| | - Graeme P Young
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, SA, Australia,
| |
Collapse
|
|
46
|
Meeks KA, Henneman P, Venema A, Burr T, Galbete C, Danquah I, Schulze MB, Mockenhaupt FP, Owusu-Dabo E, Rotimi CN, Addo J, Smeeth L, Bahendeka S, Spranger J, Mannens MM, Zafarmand MH, Agyemang C, Adeyemo A. An epigenome-wide association study in whole blood of measures of adiposity among Ghanaians: the RODAM study. Clin Epigenetics 2017; 9:103. [PMID: 28947923 PMCID: PMC5609006 DOI: 10.1186/s13148-017-0403-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/05/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Epigenome-wide association studies (EWAS) have identified DNA methylation loci involved in adiposity. However, EWAS on adiposity in sub-Saharan Africans are lacking despite the high burden of adiposity among African populations. We undertook an EWAS for anthropometric indices of adiposity among Ghanaians aiming to identify DNA methylation loci that are significantly associated. METHODS The Illumina 450k DNA methylation array was used to profile DNA methylation in whole blood samples of 547 Ghanaians from the Research on Obesity and Diabetes among African Migrants (RODAM) study. Differentially methylated positions (DMPs) and differentially methylation regions (DMRs) were identified for BMI and obesity (BMI ≥ 30 kg/m2), as well as for waist circumference (WC) and abdominal obesity (WC ≥ 102 cm in men, ≥88 cm in women). All analyses were adjusted for age, sex, blood cell distribution estimates, technical covariates, recruitment site and population stratification. We also did a replication study of previously reported EWAS loci for anthropometric indices in other populations. RESULTS We identified 18 DMPs for BMI and 23 for WC. For obesity and abdominal obesity, we identified three and one DMP, respectively. Fourteen DMPs overlapped between BMI and WC. DMP cg00574958 annotated to gene CPT1A was the only DMP associated with all outcomes analysed, attributing to 6.1 and 5.6% of variance in obesity and abdominal obesity, respectively. DMP cg07839457 (NLRC5) and cg20399616 (BCAT1) were significantly associated with BMI, obesity and with WC and had not been reported by previous EWAS on adiposity. CONCLUSIONS This first EWAS for adiposity in Africans identified three epigenome-wide significant loci (CPT1A, NLRC5 and BCAT1) for both general adiposity and abdominal adiposity. The findings are a first step in understanding the role of DNA methylation in adiposity among sub-Saharan Africans. Studies on other sub-Saharan African populations as well as translational studies are needed to determine the role of these DNA methylation variants in the high burden of adiposity among sub-Saharan Africans.
Collapse
Affiliation(s)
- Karlijn A.C. Meeks
- Department of Public Health, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Tom Burr
- Source BioScience, 1 Orchard Place, Nottingham Business Park, Nottingham, NG8 6PX UK
| | - Cecilia Galbete
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Ina Danquah
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
- Institute for Social Medicine, Epidemiology and Health Economics, Charité – Universitaetsmedizin Berlin, Berlin, Germany
| | - Matthias B. Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Frank P. Mockenhaupt
- Institute of Tropical Medicine and International Health, Charité – University Medicine Berlin, Campus Virchow-Klinikum Augustenburger Platz 1, 13353 Berlin, Germany
| | - Ellis Owusu-Dabo
- Department of Global and International Health, School of Public Health; Kumasi Centre for collaborative Research, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti Region Ghana
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, MSC 5635, Bethesda, MD 20892-5635 USA
| | - Juliet Addo
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Liam Smeeth
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | | | - Joachim Spranger
- Department of Endocrinology and Metabolism, Charité – University Medicine Berlin, Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Berlin, Germany
- Center for Cardiovascular Research (CCR), Charité – University Medicine Berlin, Berlin, Germany
| | - Marcel M.A.M. Mannens
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Mohammad H. Zafarmand
- Department of Public Health, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public Health, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, MSC 5635, Bethesda, MD 20892-5635 USA
| |
Collapse
|
|
47
|
Murray DH, Baker RT, Gaur S, Young GP, Pedersen SK. Validation of a Circulating Tumor-Derived DNA Blood Test for Detection of Methylated BCAT1 and IKZF1 DNA. J Appl Lab Med 2017; 2:165-175. [PMID: 32630973 DOI: 10.1373/jalm.2017.023135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/30/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND Colvera™ is a test that detects circulating tumor-derived DNA in patients with colorectal cancer by assaying for the presence of methylated BCAT1 and IKZF1 in blood. This study describes the analytical and clinical performance characteristics of the test. METHODS Validation was performed in accordance with ISO15189 and National Pathology Accreditation Advisory Council requirements. Spiked samples including 264 plasma and 120 buffer samples were randomized, divided into 8 batches of 48 samples, and processed over 8 days using 2 equipment lines (each line consisting of a QIAsymphony SP/AS, QIACube HT, and LC480); 2 reagent batches; and 2 operators to determine limit of detection, selectivity/specificity, precision, reproducibility, ruggedness, and susceptibility to commonly known interfering substances. Clinical performance was validated by assaying 222 archived plasma samples from subjects (n = 26 with cancer) enrolled in a previous prospective trial. RESULTS The limit of detection for Colvera was 12.6 pg/mL (95% CI, 8.6-23.9 pg/mL), which equates to 2 diploid genome copies per milliliter plasma. No statistically significant difference was determined between testing days (n = 8), instrumentation, operators, or reagent batches in precision studies for the methylation-specific assays. The assay performance was unaffected by 9 commonly known interference substances, variations in bisulfite conversion, or quantitative PCR settings (cycling temperatures, incubation times, and oligonucleotide concentrations). For this clinical cohort, sensitivity and specificity estimates for Colvera were 73.1% (19 of 26; 95% CI, 52.2-88.4) and 89.3% (175 of 196; 95% CI, 84.1-93.2), respectively. CONCLUSION Colvera is a robust test and suitable for detection of circulating tumor-derived DNA by measuring levels of methylated BCAT1 and IKZF1 in human blood plasma.
Collapse
Affiliation(s)
- David H Murray
- Clinical Genomics Pty Ltd, North Ryde, New South Wales, Australia
| | - Rohan T Baker
- Clinical Genomics Pty Ltd, North Ryde, New South Wales, Australia
| | - Snigdha Gaur
- Clinical Genomics Pty Ltd, North Ryde, New South Wales, Australia
| | - Graeme P Young
- Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, South Australia, Australia
| | | |
Collapse
|
|
48
|
Singh MP, Rai S, Suyal S, Singh SK, Singh NK, Agarwal A, Srivastava S. Genetic and epigenetic markers in colorectal cancer screening: recent advances. Expert Rev Mol Diagn 2017; 17:665-685. [PMID: 28562109 DOI: 10.1080/14737159.2017.1337511] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Colorectal cancer (CRC) is a heterogenous disease which develops from benign intraepithelial lesions known as adenomas to malignant carcinomas. Acquired alterations in Wnt signaling, TGFβ, MAPK pathway genes and clonal propagation of altered cells are responsible for this transformation. Detection of adenomas or early stage cancer in asymptomatic patients and better prognostic and predictive markers is important for improving the clinical management of CRC. Area covered: In this review, the authors have evaluated the potential of genetic and epigenetic alterations as markers for early detection, prognosis and therapeutic predictive potential in the context of CRC. We have discussed molecular heterogeneity present in CRC and its correlation to prognosis and response to therapy. Expert commentary: Molecular marker based CRC screening methods still fail to gain trust of clinicians. Invasive screening methods, molecular heterogeneity, chemoresistance and low quality test samples are some key challenges which need to be addressed in the present context. New sequencing technologies and integrated omics data analysis of individual or population cohort results in GWAS. MPE studies following a GWAS could be future line of research to establish accurate correlations between CRC and its risk factors. This strategy would identify most reliable biomarkers for CRC screening and management.
Collapse
Affiliation(s)
- Manish Pratap Singh
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Sandhya Rai
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Shradha Suyal
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Sunil Kumar Singh
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Nand Kumar Singh
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Akash Agarwal
- b Department of Surgical Oncology , Dr. Ram Manohar Lohia Institute of Medical Sciences (DRMLIMS) , Lucknow , India
| | - Sameer Srivastava
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| |
Collapse
|
|
49
|
Liu HY, Zhang CJ. Identification of differentially expressed genes and their upstream regulators in colorectal cancer. Cancer Gene Ther 2017; 24:244-250. [DOI: 10.1038/cgt.2017.8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/23/2017] [Accepted: 03/03/2017] [Indexed: 12/17/2022]
|
|
50
|
Perakis S, Auer M, Belic J, Heitzer E. Advances in Circulating Tumor DNA Analysis. Adv Clin Chem 2017; 80:73-153. [PMID: 28431643 DOI: 10.1016/bs.acc.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
Collapse
Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
| |
Collapse
|