101
|
Abstract
During cancer progression and treatment, multiple subclonal populations of tumour cells compete with one another, with selective pressures leading to the emergence of predominant subclones that replicate and spread most proficiently, and are least susceptible to treatment. At present, the molecular landscapes of solid tumours are established using surgical or biopsy tissue samples. Tissue-based tumour profiles are, however, subject to sampling bias, provide only a snapshot of tumour heterogeneity, and cannot be obtained repeatedly. Genomic profiles of circulating cell-free tumour DNA (ctDNA) have been shown to closely match those of the corresponding tumours, with important implications for both molecular pathology and clinical oncology. Analyses of circulating nucleic acids, commonly referred to as 'liquid biopsies', can be used to monitor response to treatment, assess the emergence of drug resistance, and quantify minimal residual disease. In addition to blood, several other body fluids, such as urine, saliva, pleural effusions, and cerebrospinal fluid, can contain tumour-derived genetic information. The molecular profiles gathered from ctDNA can be further complemented with those obtained through analysis of circulating tumour cells (CTCs), as well as RNA, proteins, and lipids contained within vesicles, such as exosomes. In this Review, we examine how different forms of liquid biopsies can be exploited to guide patient care and should ultimately be integrated into clinical practice, focusing on liquid biopsy of ctDNA - arguably the most clinically advanced approach.
Collapse
|
102
|
|
103
|
Shigeyasu K, Toden S, Zumwalt TJ, Okugawa Y, Goel A. Emerging Role of MicroRNAs as Liquid Biopsy Biomarkers in Gastrointestinal Cancers. Clin Cancer Res 2017; 23:2391-2399. [PMID: 28143873 DOI: 10.1158/1078-0432.ccr-16-1676] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 12/27/2016] [Accepted: 12/27/2016] [Indexed: 12/17/2022]
Abstract
Cancer has emerged as a leading cause of mortality worldwide, claiming more than 8 million lives annually. Gastrointestinal cancers account for about 35% of these mortalities. Recent advances in diagnostic and treatment strategies have reduced mortality among patients with gastrointestinal cancer, yet a significant number of patients still develop late-stage cancer, where treatment options are inadequate. Emerging interests in "liquid biopsies" have encouraged investigators to identify and develop clinically relevant noninvasive genomic and epigenomic signatures that can be exploited as biomarkers capable of detecting premalignant and early-stage cancers. In this context, microRNAs (miRNA), which are small, noncoding RNAs that are frequently dysregulated in cancers, have emerged as promising entities for such diagnostic purposes. Even though the future looks promising, current approaches for detecting miRNAs in blood and other biofluids remain inadequate. This review summarizes existing efforts to exploit circulating miRNAs as cancer biomarkers and evaluates their potential and challenges as liquid biopsy-based biomarkers for gastrointestinal cancers. Clin Cancer Res; 23(10); 2391-9. ©2017 AACR.
Collapse
Affiliation(s)
- Kunitoshi Shigeyasu
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Shusuke Toden
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Timothy J Zumwalt
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas.
| |
Collapse
|
104
|
Abstract
Colorectal carcinoma (CRC) is a common cause of morbidity and mortality worldwide. Two pathogenic pathways are involved in the development of adenoma to CRC. The first pathway involvesAPC/β-catenin characterized by chromosomal instability resulting in the accumulation of mutations. The second pathway is characterized by lesions inDNA mismatch repair genes. Aberrant DNA methylation in selected gene promoters has emerged as a new epigenetic pathway in CRC development. CRC screening is the most efficient strategy to reduce death. Specific DNA methylation events occur in multistep carcinogenesis. Epigenetic gene silencing is a causative factor of CRC development. DNA methylations have been extensively examined in stool from CRC and precursor lesions. Many methylated genes have been described in CRC and adenoma, although no definite DNA methylation biomarkers panel has been established. Multiple DNA methylation biomarkers, including secreted frizzled-related protein 2, secreted frizzled-related protein 1, tissue factor pathway inhibitor 2, vimentin, and methylguanine DNA methyltransferase, have been further investigated, and observations have revealed that DNA methylation biomarkers exhibit with high sensitivity and specificity. These markers may also be used to diagnose CRC and adenoma in early stages. Real time polymerase chain reaction (qPCR) is sensitive, scalable, specific, reliable, time saving, and cost effective. Stool exfoliated markers provide advantages, including sensitivity and specificity. A stool qPCR methylation test may also be an enhanced tool for CRC and adenoma screening.
Collapse
Affiliation(s)
- Ji-Jun Chen
- Research & Development, Allonger LLC, Columbia 21045, MD, USA.,Mei Chen Biotechnology Co. Ltd., Qingdao 266012, China
| | - Ai-Qin Wang
- The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Qing-Qi Chen
- The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| |
Collapse
|
105
|
Perkins G, Lu H, Garlan F, Taly V. Droplet-Based Digital PCR: Application in Cancer Research. Adv Clin Chem 2016; 79:43-91. [PMID: 28212714 DOI: 10.1016/bs.acc.2016.10.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The efficient characterization of genetic and epigenetic alterations in oncology, virology, or prenatal diagnostics requires highly sensitive and specific high-throughput approaches. Nevertheless, with the use of conventional methods, sensitivity and specificity were largely limited. By partitioning individual target molecules within distinct compartments, digital PCR (dPCR) could overcome these limitations and detect very rare sequences with unprecedented precision and sensitivity. In dPCR, the sample is diluted such that each individual partition will contain no more than one target sequence. Following the assay reaction, the dPCR process provides an absolute value and analyzable quantitative data. The recent coupling of dPCR with microfluidic systems in commercial platforms should lead to an essential tool for the management of patients with cancer, especially adapted to the analysis of precious samples. Applications in cancer research range from the analysis of tumor heterogeneity to that of a range of body fluids. Droplet-based dPCR is indeed particularly appropriate for the emerging field of liquid biopsy analysis. In this review, following an overview of the development in dPCR technology and different strategies based on the use of microcompartments, we will focus particularly on the applications and latest development of microfluidic droplet-based dPCR in oncology.
Collapse
Affiliation(s)
- G Perkins
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France; European Georges Pompidou Hospital, AP-HP - Paris Descartes University, Paris, France
| | - H Lu
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France
| | - F Garlan
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France
| | - V Taly
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France.
| |
Collapse
|
106
|
Williams CD, Grady WM, Zullig LL. Use of NCCN Guidelines, Other Guidelines, and Biomarkers for Colorectal Cancer Screening. J Natl Compr Canc Netw 2016; 14:1479-1485. [PMID: 27799515 PMCID: PMC5117951 DOI: 10.6004/jnccn.2016.0154] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/31/2016] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) remains a common cancer and significant public health burden. CRC-related mortality is declining, partly due to the early detection of CRC through robust screening. NCCN has established the NCCN Guidelines for CRC Screening to help healthcare providers make appropriate screening recommendations according to the patient's risk of developing CRC. This review describes the evolution of CRC screening guidelines for average-risk individuals, discusses the role of NCCN Guidelines for CRC Screening in cancer prevention, and comments on the current and emerging use of biomarkers for CRC screening.
Collapse
Affiliation(s)
- Christina D. Williams
- Cooperative Studies Program Epidemiology Center-Durham, Durham VA Medical Center, Durham, NC, USA
- Division of Medical Oncology, Duke University Medical Center, Durham, NC, USA
| | - William M. Grady
- Clinical Research Division, Fred Hutchison Cancer Research Center, University of Washington, Seattle, Washington, USA
- Center for Health Services Research in Primary Care, Durham VA Medical Center, Durham, NC, USA
| | - Leah L. Zullig
- Center for Health Services Research in Primary Care, Durham VA Medical Center, Durham, NC, USA
- Division of General Internal Medicine, Duke University Medical Center, Durham, NC, USA
| |
Collapse
|
107
|
De Rosa M, Rega D, Costabile V, Duraturo F, Niglio A, Izzo P, Pace U, Delrio P. The biological complexity of colorectal cancer: insights into biomarkers for early detection and personalized care. Therap Adv Gastroenterol 2016; 9:861-886. [PMID: 27803741 PMCID: PMC5076770 DOI: 10.1177/1756283x16659790] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Colorectal cancer has been ranked the third and second most prevalent of all cancers in men and women, respectively, and it represents the fourth most common cause of cancer deaths. In 2012, there were 1.4 million estimated cases of colorectal cancer worldwide, and 700,000 estimated deaths, which implies significant impact on public health, especially in economically-developed countries. In recent years, there has been an increase in the number of tumors, although this has been accompanied by decreased mortality, due to more appropriate and available information, earlier diagnosis, and improvements in treatment. Colorectal cancers are characterized by great genotypic and phenotypic heterogeneity, including tumor microenvironment and interactions between healthy and cancer cells. All of these traits confer a unique peculiarity to each tumor, which can thus be considered as an individual disease. Well conducted molecular and clinical characterization of each colorectal cancer is essential with a view to the implementation of precision oncology, and thus personalized care. This last aims at standardization of therapeutic plans chosen according to the genetic background of each specific neoplasm, to increase overall survival and reduce treatment side effects. Thus, prognostic and predictive molecular biomarkers assume a critical role in the characterization of colorectal cancer and in the determination of the most appropriate therapy.
Collapse
Affiliation(s)
- Marina De Rosa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples ‘Federico II ’, I-80131 Naples, Italy
| | - Daniela Rega
- Colorectal Surgical Oncology-Abdominal Oncology Department, Istituto Nazionale per lo Studio e la Cura dei Tumori, ‘Fondazione Giovanni Pascale’ IRCCS, I-80131 Naples, Italy
| | - Valeria Costabile
- Department of Molecular Medicine and Medical Biotechnology, University of Naples ‘Federico II ’, I-80131 Naples, Italy
| | - Francesca Duraturo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples ‘Federico II ’, I-80131 Naples, Italy
| | - Antonello Niglio
- Colorectal Surgical Oncology-Abdominal Oncology Department, Istituto Nazionale per lo Studio e la Cura dei Tumori, ‘Fondazione Giovanni Pascale’ IRCCS, I-80131 Naples, Italy
| | - Paola Izzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples ‘Federico II ’, I-80131 Naples, Italy
| | - Ugo Pace
- Colorectal Surgical Oncology-Abdominal Oncology Department, Istituto Nazionale per lo Studio e la Cura dei Tumori, ‘Fondazione Giovanni Pascale’ IRCCS, I-80131 Naples, Italy
| | - Paolo Delrio
- Colorectal Surgical Oncology-Abdominal Oncology Department, Istituto Nazionale per lo Studio e la Cura dei Tumori, ‘Fondazione Giovanni Pascale’ IRCCS, I-80131 Naples, Italy
| |
Collapse
|
108
|
Digital quantification of gene methylation in stool DNA by emulsion-PCR coupled with hydrogel immobilized bead-array. Biosens Bioelectron 2016; 92:596-601. [PMID: 27829567 DOI: 10.1016/j.bios.2016.10.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/08/2016] [Accepted: 10/19/2016] [Indexed: 01/04/2023]
Abstract
Aberrations of gene methylation in stool DNA (sDNA) is an effective biomarker for non-invasive colorectal cancer diagnosis. However, it is challenging to accurately quantitate the gene methylation levels in sDNA due to the low abundance and degradation of sDNA. In this study, a digital quantification strategy was proposed by combining emulsion PCR (emPCR) with hydrogel immobilized bead-array. The assay includes following steps: bisulfite conversion of sDNA, pre-amplification by PCR with specific primers containing 5' universal sequences, emPCR of pre-amplicons with beaded primers to achieve single-molecular amplification and identification of hydrogel embedding beads coated with amplicons. The sensitivity and the specificity of the method are high enough to pick up 0.05% methylated targets from unmethylated DNA background. The successful detection of hypermethylated vimentin gene in clinical stool samples suggests that the proposed method should be a potential tool for non-invasive colorectal cancer screening.
Collapse
|
109
|
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Recent implementation of low-dose computed tomography (LDCT) screening is predicted to lead to diagnosis of lung cancer at an earlier stage, with survival benefit. However, there is still a pressing need for biomarkers that will identify individuals eligible for screening, as well as improve the diagnostic accuracy of LDCT. In addition, biomarkers for prognostic stratification of patients with early stage disease, and those that can be used as surrogates to monitor tumor evolution, will greatly improve clinical management. Molecular alterations found in the DNA of tumor cells, such as mutations, translocations and methylation, are reflected in DNA that is released from the tumor into the bloodstream. Thus, in recent years, circulating tumor DNA (ctDNA) has gained increasing attention as a noninvasive alternative to tissue biopsies and potential surrogate for the entire tumor genome. Activating gene mutations found in ctDNA have been proven effective in predicting response to targeted therapy. Analysis of ctDNA is also a valuable tool for longitudinal follow-up of cancer patients that does not require serial biopsies and may anticipate the acquisition of resistance. DNA methylation has also emerged as a promising marker for early detection, prognosis and real-time follow-up of tumor dynamics that is independent of the genomic composition of the primary tumor. This review summarizes the various investigational applications of methylated ctDNA in lung cancer reported to date. It also provides a brief overview of the technologies for analysis of DNA methylation in liquid biopsies, and the challenges that befall the implementation of methylated ctDNA into routine clinical practice.
Collapse
Affiliation(s)
- Delphine Lissa
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| |
Collapse
|
110
|
Manne U, Jadhav T, Putcha BDK, Samuel T, Soni S, Shanmugam C, Suswam EA. Molecular Biomarkers of Colorectal Cancer and Cancer Disparities: Current Status and Perspective. CURRENT COLORECTAL CANCER REPORTS 2016. [PMID: 28626361 DOI: 10.1007/s11888-016-0338-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This review provides updates on the efforts for the development of prognostic and predictive markers in colorectal cancer based on the race/ethnicity of patients. Since the clinical consequences of genetic and molecular alterations differ with patient race and ethnicity, the usefulness of these molecular alterations as biomarkers needs to be evaluated in different racial/ethnic groups. To accomplish personalized patient care, a combined analysis of multiple molecular alterations in DNA, RNA, microRNAs (miRNAs), metabolites, and proteins in a single test is required to assess disease status in a precise way. Therefore, a special emphasis is placed on issues related to utility of recently identified genetic and molecular alterations in genes, miRNAs, and various "-omes" (e.g., proteomes, kinomes, metabolomes, exomes, methylomes) as candidate molecular markers to determine cancer progression (disease recurrence/relapse and metastasis) and to assess the efficacy of therapy in colorectal cancer in relation to patient race and ethnicity. This review will be useful for oncologists, pathologists, and basic and translational researchers.
Collapse
Affiliation(s)
- Upender Manne
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Comprehensive Cancer Center, Wallace Tumor Institute, University of Alabama at Birmingham, Room # 420A, 1530 3rd Avenue South, Birmingham, AL 35294, USA
| | - Trafina Jadhav
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,Wallace Tumor Institute, University of Alabama at Birmingham, Room # 430A, 1530 3rd Avenue South, Birmingham, AL 35294, USA.,Present address: Division of Cardiovascular Medicine, Vanderbilt University, 1215 21st Avenue South, Medical Center East, Suite 5050, Nashville, TN 37232-8802, USA
| | - Balananda-Dhurjati Kumar Putcha
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,Wallace Tumor Institute, University of Alabama at Birmingham, Room # 430A, 1530 3rd Avenue South, Birmingham, AL 35294, USA.,Present address: 2502 East Woodlands, Saint Joseph, MO 64506, USA
| | - Temesgen Samuel
- Department of Pathobiology, College of Veterinary Medicine, Nursing and Allied Health, Tuskegee University, Tuskegee, AL 36088, USA
| | - Shivani Soni
- Department of Biological Sciences, Alabama State University, Room # 325, Life Science Building, 1627, Hall Street, Montgomery, AL 36104, USA
| | - Chandrakumar Shanmugam
- Wallace Tumor Institute, University of Alabama at Birmingham, Room # 430A, 1530 3rd Avenue South, Birmingham, AL 35294, USA.,Present address: Department of Pathology, ESIC Medical College and Hospital, Sanathnagar, Hyderabad, Telangana 500 038, India
| | - Esther A Suswam
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Pathology, Wallace Tumor Institute, University of Alabama at Birmingham, 1720 2nd Avenue South, # 410C, Birmingham, AL 35294-3300, USA
| |
Collapse
|
111
|
Dahl E, Kloten V. [Liquid biopsy analysis using cell-free DNA (cfDNA): Opportunities and limitations]. DER PATHOLOGE 2016; 36:572-8. [PMID: 26395890 DOI: 10.1007/s00292-015-0078-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Molecular biological analysis of nucleic acids in blood or other bodily fluids (i.e. liquid biopsy analyses) may supplement the pathologists' diagnostic armamentarium in a reasonable way-particularly in cancer precision medicine. Within the field of oncology, liquid biopsy can potentially be used to monitor tumor burden in the blood and to early detect emerging resistance in the course of targeted cancer therapies. An already approved application of liquid biopsy is the detection of epidermal growth factor receptor (EGFR) driver mutations in blood samples of lung cancer patients in those cases where no tissue biopsy is available. However, there is still currently considerable insecurity associated with blood-based DNA analytic methods that must be solved before liquid biopsy can be implemented for broader routine application in the diagnosis of cancer. In this article, the current state of development of liquid biopsy in molecular diagnostics from a pathology point of view is presented.
Collapse
Affiliation(s)
- E Dahl
- Arbeitsgruppe Molekulare Onkologie, Institut für Pathologie, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland. .,Molekularpathologische Diagnostik, Institut für Pathologie, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland. .,RWTH zentralisierte Biomaterialbank (RWTH cBMB), Institut für Pathologie, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland.
| | - V Kloten
- Arbeitsgruppe Molekulare Onkologie, Institut für Pathologie, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland.
| |
Collapse
|
112
|
A Genome-Wide Methylation Approach Identifies a New Hypermethylated Gene Panel in Ulcerative Colitis. Int J Mol Sci 2016; 17:ijms17081291. [PMID: 27517910 PMCID: PMC5000688 DOI: 10.3390/ijms17081291] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/26/2016] [Accepted: 08/03/2016] [Indexed: 12/12/2022] Open
Abstract
The cause of inflammatory bowel disease (IBD) is still unknown, but there is growing evidence that environmental factors such as epigenetic changes can contribute to the disease etiology. The aim of this study was to identify newly hypermethylated genes in ulcerative colitis (UC) using a genome-wide DNA methylation approach. Using an Infinium HumanMethylation450 BeadChip array, we screened the DNA methylation changes in three normal colon controls and eight UC patients. Using these methylation profiles, 48 probes associated with CpG promoter methylation showed differential hypermethylation between UC patients and normal controls. Technical validations for methylation analyses in a larger series of UC patients (n = 79) were performed by methylation-specific PCR (MSP) and bisulfite sequencing analysis. We finally found that three genes (FAM217B, KIAA1614 and RIBC2) that were significantly elevating the promoter methylation levels in UC compared to normal controls. Interestingly, we confirmed that three genes were transcriptionally silenced in UC patient samples by qRT-PCR, suggesting that their silencing is correlated with the promoter hypermethylation. Pathway analyses were performed using GO and KEGG databases with differentially hypermethylated genes in UC. Our results highlight that aberrant hypermethylation was identified in UC patients which can be a potential biomarker for detecting UC. Moreover, pathway-enriched hypermethylated genes are possibly implicating important cellular function in the pathogenesis of UC. Overall, this study describes a newly hypermethylated gene panel in UC patients and provides new clinical information that can be used for the diagnosis and therapeutic treatment of IBD.
Collapse
|
113
|
Garrigou S, Perkins G, Garlan F, Normand C, Didelot A, Le Corre D, Peyvandi S, Mulot C, Niarra R, Aucouturier P, Chatellier G, Nizard P, Perez-Toralla K, Zonta E, Charpy C, Pujals A, Barau C, Bouché O, Emile JF, Pezet D, Bibeau F, Hutchison JB, Link DR, Zaanan A, Laurent-Puig P, Sobhani I, Taly V. A Study of Hypermethylated Circulating Tumor DNA as a Universal Colorectal Cancer Biomarker. Clin Chem 2016; 62:1129-39. [DOI: 10.1373/clinchem.2015.253609] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/28/2016] [Indexed: 12/18/2022]
Abstract
Abstract
BACKGROUND
Circulating tumor DNA (ctDNA) has emerged as a good candidate for tracking tumor dynamics in different cancer types, potentially avoiding repeated tumor biopsies. Many different genes can be mutated within a tumor, complicating procedures for tumor monitoring, even with highly sensitive next-generation sequencing (NGS) strategies. Droplet-based digital PCR (dPCR) is a highly sensitive and quantitative procedure, allowing detection of very low amounts of circulating tumor genetic material, but can be limited in the total number of target loci monitored.
METHODS
We analyzed hypermethylation of 3 genes, by use of droplet-based dPCR in different stages of colorectal cancer (CRC), to identify universal markers for tumor follow-up.
RESULTS
Hypermethylation of WIF1 (WNT inhibitory factor 1) and NPY (neuropeptide Y) genes was significantly higher in tumor tissue compared to normal tissue, independently of tumor stage. All tumor tissues appeared positive for one of the 2 markers. Methylated ctDNA (MetctDNA) was detected in 80% of metastatic CRC and 45% of localized CRC. For samples with detectable mutations in ctDNA, MetctDNA and mutant ctDNA (MutctDNA) fractions were correlated. During follow-up of different stage CRC patients, MetctDNA changes allowed monitoring of tumor evolution.
CONCLUSIONS
These results indicate that MetctDNA could be used as a universal surrogate marker for tumor follow-up in CRC patients, and monitoring MetctDNA by droplet-based dPCR could avoid the need for monitoring mutations.
Collapse
Affiliation(s)
- Sonia Garrigou
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
| | - Geraldine Perkins
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
- Department of Digestive Oncology, AP-HP, European Georges Pompidou Hospital, Paris Descartes University, Paris, France
| | - Fanny Garlan
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
| | - Corinne Normand
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
| | - Audrey Didelot
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
| | - Delphine Le Corre
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
| | - Sanam Peyvandi
- Department of Gastroenterology, Henri-Mondor Hospital-APHP and EA 7375-EC2M3 Laboratory, University of Paris Est Creteil Val de Marne, Creteil, France
| | - Claire Mulot
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
- CRB Epigenetec, INSERM UMR-S1147, Centre Universitaire des Saints-Pères, Paris Cedex 06, France
| | - Ralph Niarra
- CIC-EC4 URC HEGP, AP-HP, Hôpitaux Universitaires Paris Ouest, Paris, France
| | | | - Gilles Chatellier
- CIC-EC4 URC HEGP, AP-HP, Hôpitaux Universitaires Paris Ouest, Paris, France
| | - Philippe Nizard
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
| | - Karla Perez-Toralla
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
| | - Eleonora Zonta
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
| | - Cecile Charpy
- Department of Gastroenterology, Henri-Mondor Hospital-APHP and EA 7375-EC2M3 Laboratory, University of Paris Est Creteil Val de Marne, Creteil, France
| | - Anais Pujals
- INSERM U955, University of Paris Est Creteil Val de Marne and Department of Pathology, AP-HP, Henri-Mondor Hospital, Créteil, France
| | | | - Olivier Bouché
- Service d'hépatogastroentérologie et de cancérologie digestive, CHU de Reims, Hôpital Robert-Debré, Reims Cedex, France
| | - Jean-François Emile
- Department of Pathology, Hôpital Ambroise Paré, AP-HP, Université de Versailles St Quentin en Yvelines, Boulogne-Billancourt, France
| | - Denis Pezet
- CHU Clermont Ferrand, Clermont Ferrand Cedex 1, France
| | - Frederic Bibeau
- Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier, France
| | | | | | - Aziz Zaanan
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
- Department of Digestive Oncology, AP-HP, European Georges Pompidou Hospital, Paris Descartes University, Paris, France
| | - Pierre Laurent-Puig
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
- Department of Biology, European Georges Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France
| | - Iradj Sobhani
- Department of Gastroenterology, Henri-Mondor Hospital-APHP and EA 7375-EC2M3 Laboratory, University of Paris Est Creteil Val de Marne, Creteil, France
| | - Valerie Taly
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC5014, Centre Universitaire des Saints-Pères, Paris Cedex 06, France. Equipe labélisée Ligue contre le cancer
| |
Collapse
|
114
|
Arbeithuber B, Makova KD, Tiemann-Boege I. Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications. DNA Res 2016; 23:547-559. [PMID: 27477585 PMCID: PMC5144678 DOI: 10.1093/dnares/dsw038] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/25/2016] [Indexed: 11/13/2022] Open
Abstract
The need in cancer research or evolutionary biology to detect rare mutations or variants present at very low frequencies (<10−5) poses an increasing demand on lowering the detection limits of available methods. Here we demonstrated that amplifiable DNA lesions introduce important error sources in ultrasensitive technologies such as single molecule PCR (smPCR) applications (e.g. droplet-digital PCR), or next-generation sequencing (NGS) based methods. Using templates with known amplifiable lesions (8-oxoguanine, deaminated 5-methylcytosine, uracil, and DNA heteroduplexes), we assessed with smPCR and duplex sequencing that templates with these lesions were amplified very efficiently by proofreading polymerases (except uracil), leading to G->T, and to a lesser extent, to unreported G->C substitutions at 8-oxoguanine lesions, and C->T transitions in amplified uracil containing templates. Long heat incubations common in many DNA extraction protocols significantly increased the number of G->T substitutions. Moreover, in ∼50-80% smPCR reactions we observed the random amplification preference of only one of both DNA strands explaining the known ‘PCR jackpot effect’, with the result that a lesion became indistinguishable from a true mutation or variant. Finally, we showed that artifactual mutations derived from uracil and 8-oxoguanine could be significantly reduced by DNA repair enzymes.
Collapse
Affiliation(s)
- Barbara Arbeithuber
- Institute of Biophysics, Johannes Kepler University, Linz 4020, Austria.,Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | | |
Collapse
|
115
|
Volik S, Alcaide M, Morin RD, Collins C. Cell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies. Mol Cancer Res 2016; 14:898-908. [DOI: 10.1158/1541-7786.mcr-16-0044] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/30/2016] [Indexed: 11/16/2022]
|
116
|
Trombetta D, Sparaneo A, Fabrizio FP, Muscarella LA. Liquid biopsy and NSCLC. Lung Cancer Manag 2016; 5:91-104. [PMID: 30643553 DOI: 10.2217/lmt-2016-0006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/20/2016] [Indexed: 12/18/2022] Open
Abstract
In the era of high-throughput molecular screening and personalized medicine, difficulty in determining whether cancer mutations are truly 'actionable' remains a gray zone in NSCLC. The most important prerequisite to perform such investigations is the tumor tissue retrieval via biopsy at diagnosis and after occurrence of resistance. Blood-based liquid biopsy as circulating tumor cells, circulating tumor DNA and exosomes can offer a fast and non-invasive method to elucidate the genetic heterogeneity of patients, the screening and patient stratification and give a dynamic surveillance for tumor progression and monitor treatments response. Here we prospectively discuss the three main approaches in the blood-biopsy field of lung cancer patients and its clinical applications in patient management. We also outline some of the analytical challenges that remain for liquid biopsy techniques in demonstrating that it could represent a true and actionable picture in lung cancer management for the implementation into clinical routine.
Collapse
Affiliation(s)
- Domenico Trombetta
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
| | - Angelo Sparaneo
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
| | - Federico Pio Fabrizio
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
| |
Collapse
|
117
|
Lam K, Pan K, Linnekamp JF, Medema JP, Kandimalla R. DNA methylation based biomarkers in colorectal cancer: A systematic review. Biochim Biophys Acta Rev Cancer 2016; 1866:106-20. [PMID: 27385266 DOI: 10.1016/j.bbcan.2016.07.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/30/2016] [Accepted: 07/01/2016] [Indexed: 12/11/2022]
Abstract
Since genetic and epigenetic alterations influence the development of colorectal cancer (CRC), huge potential lies in the use of DNA methylation as biomarkers to improve the current diagnosis, screening, prognosis and treatment prediction. Here we performed a systematic review on DNA methylation-based biomarkers published in CRC, and discussed the current state of findings and future challenges. Based on the findings, we then provide a perspective on future studies. Genome-wide studies on DNA methylation revealed novel biomarkers as well as distinct subgroups that exist in CRC. For diagnostic purposes, the most independently validated genes to study further are VIM, SEPT9, ITGA4, OSM4, GATA4 and NDRG4. These hypermethylated biomarkers can even be combined with LINE1 hypomethylation and the performance of markers should be examined in comparison to FIT further to find sensitive combinations. In terms of prognostic markers, myopodin, KISS1, TMEFF2, HLTF, hMLH1, APAF1, BCL2 and p53 are independently validated. Most prognostic markers published lack both a multivariate analysis in comparison to clinical risk factors and the appropriate patient group who will benefit by adjuvant chemotherapy. Methylation of IGFBP3, mir148a and PTEN are found to be predictive markers for 5-FU and EGFR therapy respectively. For therapy prediction, more studies should focus on finding markers for chemotherapeutic drugs as majority of the patients would benefit. Translation of these biomarkers into clinical utility would require large-scale prospective cohorts and randomized clinical trials in future. Based on these findings and consideration we propose an avenue to introduce methylation markers into clinical practice in near future. For future studies, multi-omics profiling on matched tissue and non-invasive cohorts along with matched cohorts of adenoma to carcinoma is indispensable to concurrently stratify CRC and find novel, robust biomarkers. Moreover, future studies should examine the timing and heterogeneity of methylation as well as the difference in methylation levels between epithelial and stromal tissues.
Collapse
Affiliation(s)
- Kevin Lam
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Kathy Pan
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Janneke Fiona Linnekamp
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Raju Kandimalla
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
118
|
Rasmussen SL, Krarup HB, Sunesen KG, Pedersen IS, Madsen PH, Thorlacius-Ussing O. Hypermethylated DNA as a biomarker for colorectal cancer: a systematic review. Colorectal Dis 2016; 18:549-61. [PMID: 26998585 DOI: 10.1111/codi.13336] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/03/2016] [Indexed: 12/11/2022]
Abstract
AIM Improved methods for early detection of colorectal cancer (CRC) are essential for increasing survival. Hypermethylated DNA in blood or stool has been proposed as a biomarker for CRC. Biochemical methods have improved in recent years, and several hypermethylated genes that are sensitive and specific for CRC have been proposed. Articles describing the use of hypermethylated promoter regions in blood or stool as biomarkers for CRC were systematically reviewed. METHOD A systematic literature search was performed using the Medline, Web of Science and Embase databases. Studies were included if they analysed hypermethylated genes from stool or blood samples in correlation with CRC. Studies in languages other than English and those based on animal models or cell lines were excluded. RESULTS The literature search yielded 74 articles, including 43 addressing blood samples and 31 addressing stool samples. In blood samples, hypermethylated ALX4, FBN2, HLTF, P16, TMEFF1 and VIM were associated with poor prognosis, hypermethylated APC, NEUROG1, RASSF1A, RASSF2A, SDC2, SEPT9, TAC1 and THBD were detected in early stage CRC and hypermethylated P16 and TFPI2 were associated with CRC recurrence. In stool samples, hypermethylated BMP3, PHACTR3, SFRP2, SPG20, TFPI2 and TMEFF2 were associated with early stage CRC. CONCLUSION Hypermethylation of the promoters of specific genes measured in blood or stool samples could be used as a CRC biomarker and provide prognostic information. The majority of studies, however, include only a few patients with poorly defined control groups. Further studies are therefore needed before hypermethylated DNA can be widely applied as a clinical biomarker for CRC detection and prognosis.
Collapse
Affiliation(s)
- S L Rasmussen
- Department of Gastrointestinal Surgery and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - H B Krarup
- Section of Molecular Diagnostics, Clinical Biochemistry and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - K G Sunesen
- Department of Gastrointestinal Surgery and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - I S Pedersen
- Section of Molecular Diagnostics, Clinical Biochemistry and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - P H Madsen
- Section of Molecular Diagnostics, Clinical Biochemistry and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - O Thorlacius-Ussing
- Department of Gastrointestinal Surgery and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| |
Collapse
|
119
|
Heimer BW, Tam BE, Minkovsky A, Sikes HD. Using nanobiotechnology to increase the prevalence of epigenotyping assays in precision medicine. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [PMID: 27126368 DOI: 10.1002/wnan.1407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/07/2016] [Accepted: 03/17/2016] [Indexed: 12/31/2022]
Abstract
Epigenetic silencing of genes that are important for DNA repair, cell cycle control, apoptosis, and cellular interactions with the extracellular matrix has been causally linked to several subtypes of cancer. Translating this knowledge of the implications of promoter methylation to wide and routine use in clinical pathology laboratories has been more challenging than the case of genetic analyses because epigenetic modifications do not change the underlying sequence of the affected nucleic acid, rendering polymerase chain reaction analysis alone uninformative. Two epigenotyping assays that detect promoter methylation are currently standard of care in treatment of two distinct tumor types in only a few top hospitals across the United States. Both rely on a harsh chemical step that degrades over 90% of tumor DNA samples, which are often available in limited quantities, and imparts the potential for false-negative or false-positive results if the reaction conditions are not exactly correct. Using nanotechnology and biotechnology to devise practical new analysis techniques that avoid the drawbacks of current techniques represents a powerful approach that is likely to significantly increase the clinical use of this class of biomarkers in the coming years. WIREs Nanomed Nanobiotechnol 2017, 9:e1407. doi: 10.1002/wnan.1407 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Brandon W Heimer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brooke E Tam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alissa Minkovsky
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
120
|
Hashimoto Y, Zumwalt TJ, Goel A. DNA methylation patterns as noninvasive biomarkers and targets of epigenetic therapies in colorectal cancer. Epigenomics 2016; 8:685-703. [PMID: 27102979 DOI: 10.2217/epi-2015-0013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aberrant DNA methylation is frequently detected in gastrointestinal tumors, and can therefore potentially be used to screen, diagnose, prognosticate, and predict colorectal cancers (CRCs). Although colonoscopic screening remains the gold standard for CRC screening, this procedure is invasive, expensive, and suffers from poor patient compliance. Methylated DNA is an attractive choice for a biomarker substrate because CRCs harbor hundreds of aberrantly methylated genes. Furthermore, abundance in extracellular environments and resistance to degradation and enrichment in serum, stool, and other noninvasive bodily fluids, allows quantitative measurements of methylated DNA biomarkers. This article describes the most important studies that investigated the efficacy of serum- or stool-derived methylated DNA as population-based screening biomarkers in CRC, details several mechanisms and factors that control DNA methylation, describes a better use of prevailing technologies that discover novel DNA methylation biomarkers, and illustrates the diversity of demethylating agents and their applicability toward clinical impact.
Collapse
Affiliation(s)
- Yutaka Hashimoto
- Center for Translational Genomics & Oncology, Baylor Scott & White Research Institute & Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Timothy J Zumwalt
- Center for Translational Genomics & Oncology, Baylor Scott & White Research Institute & Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Ajay Goel
- Center for Translational Genomics & Oncology, Baylor Scott & White Research Institute & Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| |
Collapse
|
121
|
Van Krieken JHJM, Rouleau E, Ligtenberg MJL, Normanno N, Patterson SD, Jung A. RAS testing in metastatic colorectal cancer: advances in Europe. Virchows Arch 2016; 468:383-96. [PMID: 26573425 PMCID: PMC4830882 DOI: 10.1007/s00428-015-1876-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 12/22/2022]
Abstract
Personalized medicine shows promise for maximizing efficacy and minimizing toxicity of anti-cancer treatment. KRAS exon 2 mutations are predictive of resistance to epidermal growth factor receptor-directed monoclonal antibodies in patients with metastatic colorectal cancer. Recent studies have shown that broader RAS testing (KRAS and NRAS) is needed to select patients for treatment. While Sanger sequencing is still used, approaches based on various methodologies are available. Few CE-approved kits, however, detect the full spectrum of RAS mutations. More recently, "next-generation" sequencing has been developed for research use, including parallel semiconductor sequencing and reversible termination. These techniques have high technical sensitivities for detecting mutations, although the ideal threshold is currently unknown. Finally, liquid biopsy has the potential to become an additional tool to assess tumor-derived DNA. For accurate and timely RAS testing, appropriate sampling and prompt delivery of material is critical. Processes to ensure efficient turnaround from sample request to RAS evaluation must be implemented so that patients receive the most appropriate treatment. Given the variety of methodologies, external quality assurance programs are important to ensure a high standard of RAS testing. Here, we review technical and practical aspects of RAS testing for pathologists working with metastatic colorectal cancer tumor samples. The extension of markers from KRAS to RAS testing is the new paradigm for biomarker testing in colorectal cancer.
Collapse
Affiliation(s)
- J Han J M Van Krieken
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands.
| | | | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, INT-Fondazione Pascale, Naples, Italy
| | - Scott D Patterson
- Amgen Inc., Thousand Oaks, CA, USA
- Gilead Sciences, Inc., Foster City, CA, USA
| | - Andreas Jung
- Institute of Pathology, University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
122
|
DING X, MU Y. Research and Application Progress of Digital Nucleic Acid Amplification Detection Techniques. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60918-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
123
|
Gu W, Crawford ED, O'Donovan BD, Wilson MR, Chow ED, Retallack H, DeRisi JL. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol 2016; 17:41. [PMID: 26944702 PMCID: PMC4778327 DOI: 10.1186/s13059-016-0904-5] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/18/2016] [Indexed: 01/04/2023] Open
Abstract
Next-generation sequencing has generated a need for a broadly applicable method to remove unwanted high-abundance species prior to sequencing. We introduce DASH (Depletion of Abundant Sequences by Hybridization). Sequencing libraries are 'DASHed' with recombinant Cas9 protein complexed with a library of guide RNAs targeting unwanted species for cleavage, thus preventing them from consuming sequencing space. We demonstrate a more than 99 % reduction of mitochondrial rRNA in HeLa cells, and enrichment of pathogen sequences in patient samples. We also demonstrate an application of DASH in cancer. This simple method can be adapted for any sample type and increases sequencing yield without additional cost.
Collapse
Affiliation(s)
- W Gu
- Departments of Pathology and Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - E D Crawford
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - B D O'Donovan
- Integrative Program in Quantitative Biology, Bioinformatics, University of California San Francisco, San Francisco, CA, USA.
| | - M R Wilson
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
| | - E D Chow
- Center for Advanced Technology, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
| | - H Retallack
- Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA.
| | - J L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
124
|
Zhai RL, Xu F, Zhang P, Zhang WL, Wang H, Wang JL, Cai KL, Long YP, Lu XM, Tao KX, Wang GB. The Diagnostic Performance of Stool DNA Testing for Colorectal Cancer: A Systematic Review and Meta-Analysis. Medicine (Baltimore) 2016; 95:e2129. [PMID: 26844449 PMCID: PMC4748866 DOI: 10.1097/md.0000000000002129] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 10/21/2015] [Accepted: 11/01/2015] [Indexed: 12/13/2022] Open
Abstract
This meta-analysis was designed to evaluate the diagnostic performance of stool DNA testing for colorectal cancer (CRC) and compare the performance between single-gene and multiple-gene tests.MEDLINE, Cochrane, EMBASE databases were searched using keywords colorectal cancers, stool/fecal, sensitivity, specificity, DNA, and screening. Sensitivity analysis, quality assessments, and performance bias were performed for the included studies.Fifty-three studies were included in the analysis with a total sample size of 7524 patients. The studies were heterogeneous with regard to the genes being analyzed for fecal genetic biomarkers of CRC, as well as the laboratory methods being used for each assay. The sensitivity of the different assays ranged from 2% to 100% and the specificity ranged from 81% to 100%. The meta-analysis found that the pooled sensitivities for single- and multigene assays were 48.0% and 77.8%, respectively, while the pooled specificities were 97.0% and 92.7%. Receiver operator curves and diagnostic odds ratios showed no significant difference between both tests with regard to sensitivity or specificity.This meta-analysis revealed that using assays that evaluated multiple genes compared with single-gene assays did not increase the sensitivity or specificity of stool DNA testing in detecting CRC.
Collapse
Affiliation(s)
- Rong-Lin Zhai
- From the Department of General Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
125
|
Dahl E, Jung A, Fassunke J, Hummel M, Penzel R, Dietmaier W, Laßmann S. [Chances and risks of blood-based molecular pathological analysis of circulating tumor cells (CTC) and cell-free DNA (cfDNA) in personalized cancer therapy: positional paper from the study group on liquid biopsy of the working group for molecular pathology in the German Society of Pathology (DGP)]. DER PATHOLOGE 2015; 36:92-7. [PMID: 25533324 DOI: 10.1007/s00292-014-2069-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- E Dahl
- Institut für Pathologie, Uniklinik RWTH Aachen, Aachen, Deutschland,
| | | | | | | | | | | | | |
Collapse
|
126
|
Shinjo K, Kondo Y. Targeting cancer epigenetics: Linking basic biology to clinical medicine. Adv Drug Deliv Rev 2015; 95:56-64. [PMID: 26494398 DOI: 10.1016/j.addr.2015.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/23/2015] [Accepted: 10/09/2015] [Indexed: 02/06/2023]
Abstract
Recent studies provide compelling evidence that epigenetic dysregulation is involved in almost every step of tumor development and progression. Differences in tumor behavior, which ultimately reflects clinical outcome, can be explained by variations in gene expression patterns generated by epigenetic mechanisms, such as DNA methylation. Therefore, epigenetic abnormalities are considered potential biomarkers and therapeutic targets. DNA methylation is stable at certain specific loci in cancer cells and predominantly reflects the characteristic clinicopathological features. Thus, it is an ideal biomarker for cancer screening, classification and prognostic purposes. Epigenetic treatment for cancers is based on the pharmacologic targeting of various core transcriptional programs that sustains cancer cell identity. Therefore, targeting aberrant epigenetic modifiers may be effective for multiple processes compared with using a selective inhibitor of aberrant single signaling pathway. This review provides an overview of the epigenetic alterations in human cancers and discusses about novel therapeutic strategies targeting epigenetic alterations.
Collapse
Affiliation(s)
- Keiko Shinjo
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Yutaka Kondo
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan.
| |
Collapse
|
127
|
Xue M, Lai SC, Xu ZP, Wang LJ. Noninvasive DNA methylation biomarkers in colorectal cancer: A systematic review. J Dig Dis 2015; 16:699-712. [PMID: 26565661 DOI: 10.1111/1751-2980.12299] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/25/2015] [Accepted: 11/08/2015] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To summarize the current evidence on the biomarkers associated with DNA methylation in the screening and diagnosis of colorectal cancer (CRC). METHODS A literature search was conducted on the databases of PubMed and Web of Science to identify articles published from 1 January 2000 to 6 June 2015 with language striction. Stuides focusing on the association between noninvasive biomarkers indicating DNA methylation and CRC were included. RESULTS Altogether 74 studies were finally included in the study. Varied genetic markers in the feces and blood samples were hypermethylated in patients with CRC than in the healthy controls. Some of them could even be detected at the early stage of the tumors. The sensitivity of the genetic markers was superior to that of fecal occult blood test and carcinoembryonic antigen. Multitarget DNA assays using a combination of different methylated genes could improve the diagnostic sensitivity. CONCLUSIONS Genetic markers might be minimally invasive, economical and accurate for the screening and surveillance of CRC. Large multicenter studies evaluating these biomarkers systematically and prospectively not only in CRC but also in other types of cancers are needed in the future.
Collapse
Affiliation(s)
- Meng Xue
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine, Zhejiang University.,Institute of Gastroenterology, Zhejiang University
| | - San Chuan Lai
- Institute of Gastroenterology, Zhejiang University.,Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zhi Peng Xu
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine, Zhejiang University
| | - Liang Jing Wang
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine, Zhejiang University.,Institute of Gastroenterology, Zhejiang University
| |
Collapse
|
128
|
Kalniņa Z, Meistere I, Kikuste I, Tolmanis I, Zayakin P, Linē A. Emerging blood-based biomarkers for detection of gastric cancer. World J Gastroenterol 2015; 21:11636-11653. [PMID: 26556992 PMCID: PMC4631966 DOI: 10.3748/wjg.v21.i41.11636] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 07/08/2015] [Accepted: 09/30/2015] [Indexed: 02/06/2023] Open
Abstract
Early detection and efficient monitoring of tumor dynamics are prerequisites for reducing disease burden and mortality, and for improving the management of patients with gastric cancer (GC). Blood-based biomarker assays for the detection of early-stage GC could be of great relevance both for population-wide or risk group-based screening programs, while circulating biomarkers that reflect the genetic make-up and dynamics of the tumor would allow monitoring of treatment efficacy, predict recurrences and assess the genetic heterogeneity of the tumor. Recent research to identify blood-based biomarkers of GC has resulted in the identification of a wide variety of cancer-associated molecules, including various proteins, autoantibodies against tumor associated antigens, cell-free DNA fragments, mRNAs and various non-coding RNAs, circulating tumor cells and cancer-derived extracellular vesicles. Each type of these biomarkers provides different information on the disease status, has different advantages and disadvantages, and distinct clinical usefulness. In the current review, we summarize the recent developments in blood-based GC biomarker discovery, discuss the origin of various types of biomarkers and their clinical usefulness and the technological challenges in the development of biomarker assays for clinical use.
Collapse
|
129
|
Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients. Cell Res 2015; 25:1250-64. [PMID: 26516143 PMCID: PMC4650428 DOI: 10.1038/cr.2015.126] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 09/09/2015] [Accepted: 09/22/2015] [Indexed: 12/17/2022] Open
Abstract
Despite advances in DNA methylome analyses of cells and tissues, current techniques for genome-scale profiling of DNA methylation in circulating cell-free DNA (ccfDNA) remain limited. Here we describe a methylated CpG tandems amplification and sequencing (MCTA-Seq) method that can detect thousands of hypermethylated CpG islands simultaneously in ccfDNA. This highly sensitive technique can work with genomic DNA as little as 7.5 pg, which is equivalent to 2.5 copies of the haploid genome. We have analyzed a cohort of tissue and plasma samples (n = 151) of hepatocellular carcinoma (HCC) patients and control subjects, identifying dozens of high-performance markers in blood for detecting small HCC (≤ 3 cm). Among these markers, 4 (RGS10, ST8SIA6, RUNX2 and VIM) are mostly specific for cancer detection, while the other 15, classified as a novel set, are already hypermethylated in the normal liver tissues. Two corresponding classifiers have been established, combination of which achieves a sensitivity of 94% with a specificity of 89% for the plasma samples from HCC patients (n = 36) and control subjects including cirrhosis patients (n = 17) and normal individuals (n = 38). Notably, all 15 alpha-fetoprotein-negative HCC patients were successfully identified. Comparison between matched plasma and tissue samples indicates that both the cancer and noncancerous tissues contribute to elevation of the methylation markers in plasma. MCTA-Seq will facilitate the development of ccfDNA methylation biomarkers and contribute to the improvement of cancer detection in a clinical setting.
Collapse
|
130
|
Xue M, Wang LJ. Value of DNA methylation markers in colorectal cancer screening. Shijie Huaren Xiaohua Zazhi 2015; 23:4626-4635. [DOI: 10.11569/wcjd.v23.i29.4626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors in the world. Recognizing CRC at an early stage by population-based screening is crucial in the prevention and treatment of CRC. Numerous candidate genes, which play important roles in the development and progression of CRC, have been found to be hyper-methylated in the promoter regions in recent studies. The promoter fragments of those hyper-methylated genes in tumor tissues have also been detected in the blood and fecal specimens, with higher sensitivity and specificity than traditional markers in the screening of CRC, including carcino-embryonic antigen (CEA) and fecal occult blood test. Here, we will discuss what we have already known about the DNA methylation markers for CRC screening and the potential research direction in the future.
Collapse
|
131
|
Dhaliwal A, Vlachostergios PJ, Oikonomou KG, Moshenyat Y. Fecal DNA testing for colorectal cancer screening: Molecular targets and perspectives. World J Gastrointest Oncol 2015; 7:178-183. [PMID: 26483873 PMCID: PMC4606173 DOI: 10.4251/wjgo.v7.i10.178] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/17/2015] [Accepted: 08/28/2015] [Indexed: 02/05/2023] Open
Abstract
The early detection of colorectal cancer with effective screening is essential for reduction of cancer-specific mortality. The addition of fecal DNA testing in the armamentarium of screening methods already in clinical use launches a new era in the noninvasive part of colorectal cancer screening and emanates from a large number of previous and ongoing clinical investigations and technological advancements. In this review, we discuss the molecular rational and most important genetic alterations hallmarking the early colorectal carcinogenesis process. Also, representative DNA targets-markers and key aspects of their testing at the clinical level in comparison or/and association with other screening methods are described. Finally, a critical view of the strengths and limitations of fecal DNA tests is provided, along with anticipated barriers and suggestions for further exploitation of their use.
Collapse
|
132
|
Developments in Screening Tests and Strategies for Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2015; 2015:326728. [PMID: 26504799 PMCID: PMC4609363 DOI: 10.1155/2015/326728] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/19/2015] [Accepted: 04/28/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND Worldwide, colorectal cancer (CRC) is the third most common cancer in men and second most common in women. It is the fourth most common cause of cancer mortality. In the United States, CRC is the third most common cause of cancer and second most common cause of cancer mortality. Incidence and mortality rates have steadily fallen, primarily due to widespread screening. METHODS We conducted keyword searches on PubMed in four categories of CRC screening: stool, endoscopic, radiologic, and serum, as well as news searches in Medscape and Google News. RESULTS Colonoscopy is the gold standard for CRC screening and the most common method in the United States. Technological improvements continue to be made, including the promising "third-eye retroscope." Fecal occult blood remains widely used, particularly outside the United States. The first at-home screen, a fecal DNA screen, has also recently been approved. Radiological methods are effective but seldom used due to cost and other factors. Serum tests are largely experimental, although at least one is moving closer to market. CONCLUSIONS Colonoscopy is likely to remain the most popular screening modality for the immediate future, although its shortcomings will continue to spur innovation in a variety of modalities.
Collapse
|
133
|
Abstract
Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. One of the fundamental processes driving the initiation and progression of CRC is the accumulation of a variety of genetic and epigenetic changes in colonic epithelial cells. Over the past decade, major advances have been made in our understanding of cancer epigenetics, particularly regarding aberrant DNA methylation, microRNA (miRNA) and noncoding RNA deregulation, and alterations in histone modification states. Assessment of the colon cancer "epigenome" has revealed that virtually all CRCs have aberrantly methylated genes and altered miRNA expression. The average CRC methylome has hundreds to thousands of abnormally methylated genes and dozens of altered miRNAs. As with gene mutations in the cancer genome, a subset of these epigenetic alterations, called driver events, are presumed to have a functional role in CRC. In addition, the advances in our understanding of epigenetic alterations in CRC have led to these alterations being developed as clinical biomarkers for diagnostic, prognostic, and therapeutic applications. Progress in this field suggests that these epigenetic alterations will be commonly used in the near future to direct the prevention and treatment of CRC.
Collapse
Affiliation(s)
- Yoshinaga Okugawa
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, TX, 75246-2017, USA
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ajay Goel
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, Texas.
| |
Collapse
|
134
|
Jiang T, Ren S, Zhou C. Role of circulating-tumor DNA analysis in non-small cell lung cancer. Lung Cancer 2015; 90:128-34. [PMID: 26415994 DOI: 10.1016/j.lungcan.2015.09.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 09/13/2015] [Indexed: 01/04/2023]
Abstract
The discovery of actionable driver mutations such as epidermal growth factor receptor (EGFR) and microtubule-associated protein-like 4 anaplastic lymphoma kinase (EML4-ALK) and their highly responses to EGFR and ALK tyrosine kinase inhibitors (TKIs) in patients with advanced non-small-cell lung cancer (NSCLC) allowed precise medicine into reality. However, a substantial part of patients still have no sufficient tissue to perform genomic analysis. As a promising noninvasive biomarker and potential surrogate for the entire tumor genome, circulating tumor DNA (ctDNA) has been applied to the detection of driver gene mutations and epigenetic alteration and monitoring of tumor burden, acquired resistance, tumor heterogeneity and early diagnosis. Since precise therapy is a strategy that optimal therapy is decided based on simultaneous tumor genome information, ctDNA, as a liquid biopsy, may help to perform dynamic genetic surveillance. In this paper we will perspectively discuss the biology and identification of ctDNA in the blood of NSCLC patients and its clinical applications in patient management.
Collapse
Affiliation(s)
- Tao Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, PR China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, PR China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, PR China.
| |
Collapse
|
135
|
Yu H, Hahn Y, Yang I. Reference Materials for Calibration of Analytical Biases in Quantification of DNA Methylation. PLoS One 2015; 10:e0137006. [PMID: 26368560 PMCID: PMC4569303 DOI: 10.1371/journal.pone.0137006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/11/2015] [Indexed: 01/04/2023] Open
Abstract
Most contemporary methods for the quantification of DNA methylation employ bisulfite conversion and PCR amplification. However, many reports have indicated that bisulfite-mediated PCR methodologies can result in inaccurate measurements of DNA methylation owing to amplification biases. To calibrate analytical biases in quantification of gene methylation, especially those that arise during PCR, we utilized reference materials that represent exact bisulfite-converted sequences with 0% and 100% methylation status of specific genes. After determining relative quantities using qPCR, pairs of plasmids were gravimetrically mixed to generate working standards with predefined DNA methylation levels at 10% intervals in terms of mole fractions. The working standards were used as controls to optimize the experimental conditions and also as calibration standards in melting-based and sequencing-based analyses of DNA methylation. Use of the reference materials enabled precise characterization and proper calibration of various biases during PCR and subsequent methylation measurement processes, resulting in accurate measurements.
Collapse
Affiliation(s)
- Hannah Yu
- Center for Bioanalysis, Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, 305–340, Republic of Korea
- Bio-analytical Science, University of Science and Technology, Daejeon, 305–340, Republic of Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul, 156–756, Republic of Korea
| | - Inchul Yang
- Center for Bioanalysis, Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, 305–340, Republic of Korea
- Bio-analytical Science, University of Science and Technology, Daejeon, 305–340, Republic of Korea
- * E-mail:
| |
Collapse
|
136
|
Jankowska AM, Millward CL, Caldwell CW. The potential of DNA modifications as biomarkers and therapeutic targets in oncology. Expert Rev Mol Diagn 2015; 15:1325-37. [PMID: 26394702 DOI: 10.1586/14737159.2015.1084229] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Knowledge of epigenetic alterations in cancer is rapidly increasing due to the development of genome-wide techniques for their identification. DNA methylation is the best understood epigenetic adaptation and disease-specific aberrant DNA methylation is a well-recognized hallmark of cancer. Recently, novel modifications, including 5-hydroxymethylation have been described, adding a new layer of complexity to understanding the epigenetic machinery and their role in cancer. There have been significant advances in techniques for the discovery and validation of DNA methylation- and hydroxymethylation-based biomarkers, each with its own advantages and limitations. With the advent of new profiling technologies, the ever-growing list of genes that show epigenetic alterations, particularly DNA methylation, emphasizes the role of these changes for early detection, diagnosis, prognosis, and prediction of response to therapies. While there are yet many challenges to the effective implementation of DNA-methylation/hydroxymethylation-based biomarkers and epigenetic therapeutics, the field is moving closer to the goal of defining personalized medicine.
Collapse
Affiliation(s)
- Anna M Jankowska
- a Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN 46285 USA
| | - Carl L Millward
- a Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN 46285 USA
| | | |
Collapse
|
137
|
|
138
|
Karapetis CS, Maru D, Waring P, Tie J, Michael MZ. Incorporating traditional and emerging biomarkers in the clinical management of metastatic colorectal cancer. Expert Rev Mol Diagn 2015; 15:1033-48. [PMID: 26166616 DOI: 10.1586/14737159.2015.1052797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The role of biomarker assessment in determining the best therapeutic options for patients with metastatic colorectal cancer has become increasingly complex and important. Biomarkers that predict the efficacy and/or toxicity of such treatments can affect medical decision making, leading to decreased harm and/or costs associated with treatment and improvements in therapeutic outcomes for patients. This review discusses traditional and emerging biomarkers of potential clinical utility for patients with metastatic colorectal cancer, current assays and methods used in clinical practice, technologies that have allowed the identification of new biomarkers and key considerations for oncologists and pathologists when determining appropriate biomarker evaluations to be undertaken for their patients.
Collapse
Affiliation(s)
- Christos S Karapetis
- Flinders Medical Centre, Sturt Road, Bedford Park, South Australia 5042, Australia
| | | | | | | | | |
Collapse
|
139
|
Li Y, Liang J, Hou P. Hypermethylation in gastric cancer. Clin Chim Acta 2015; 448:124-32. [PMID: 26148722 DOI: 10.1016/j.cca.2015.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 07/02/2015] [Accepted: 07/02/2015] [Indexed: 02/07/2023]
Abstract
Although gastric cancer (GC) is highly prevalent in China and is a leading cause of cancer-related death, major advances in early diagnostic and effective therapeutic strategies have not been made. GC patients are usually diagnosed at an advanced stage and the prognosis is still poor. Over the years, many efforts have been done on exploring the pathology of GC. In particular, genome-wide analysis tools have been widely used in the detection of genetic and epigenetic alterations in GC. For example, many tumor suppressor genes have been found to be aberrantly hypermethylated in GCs, and some even in gastric precancerous lesions, suggesting a role of this molecular event in early gastric tumorigenesis. In addition, accumulating evidences have demonstrated that some hypermethylated genes can be used as potential biomarkers for detection and diagnosis of GC in biopsy specimens and non-invasive body fluids. These exciting advances provide unprecedented opportunities for the development of molecular-based novel diagnostic, prognostic, and therapeutic strategies for GC. Here, we reviewed recent findings on the promoter hypermethylation of tumor suppressor genes in GC and aimed to provide better understanding of the contribution of this epigenetic event to gastric tumorigenesis.
Collapse
Affiliation(s)
- Yujun Li
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, People's Republic of China
| | - Junrong Liang
- Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, People's Republic of China
| | - Peng Hou
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, People's Republic of China.
| |
Collapse
|
140
|
Wielscher M, Vierlinger K, Kegler U, Ziesche R, Gsur A, Weinhäusel A. Diagnostic Performance of Plasma DNA Methylation Profiles in Lung Cancer, Pulmonary Fibrosis and COPD. EBioMedicine 2015; 2:929-36. [PMID: 26425700 PMCID: PMC4563135 DOI: 10.1016/j.ebiom.2015.06.025] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 06/23/2015] [Accepted: 06/26/2015] [Indexed: 12/17/2022] Open
Abstract
Disease-specific alterations of the cell-free DNA methylation status are frequently found in serum samples and are currently considered to be suitable biomarkers. Candidate markers were identified by bisulfite conversion-based genome-wide methylation screening of lung tissue from lung cancer, fibrotic ILD, and COPD. cfDNA from 400 μl serum (n = 204) served to test the diagnostic performance of these markers. Following methylation-sensitive restriction enzyme digestion and enrichment of methylated DNA via targeted amplification (multiplexed MSRE enrichment), a total of 96 markers were addressed by highly parallel qPCR. Lung cancer was efficiently separated from non-cancer and controls with a sensitivity of 87.8%, (95%CI: 0.67–0.97) and specificity 90.2%, (95%CI: 0.65–0.98). Cancer was distinguished from ILD with a specificity of 88%, (95%CI: 0.57–1), and COPD from cancer with a specificity of 88% (95%CI: 0.64–0.97). Separation of ILD from COPD and controls was possible with a sensitivity of 63.1% (95%CI: 0.4–0.78) and a specificity of 70% (95%CI: 0.54–0.81). The results were confirmed using an independent sample set (n = 46) by use of the four top markers discovered in the study (HOXD10, PAX9, PTPRN2, and STAG3) yielding an AUC of 0.85 (95%CI: 0.72–0.95). This technique was capable of distinguishing interrelated complex pulmonary diseases suggesting that multiplexed MSRE enrichment might be useful for simple and reliable diagnosis of diverse multifactorial disease states. The multiplexed MSRE enrichment strategy allowed a highly parallel assessment the cfDNA methylation status based on 400 μl of patient serum. The multivariate classification of the discovered biomarkers, thus, stabilized the prediction and allowed for differential diagnosis. This method including the biomarker set may be used to monitor the lung cancer risk in COPD and fibrotic ILD patients.
Research in Context We developed a multiplexed DNA methylation profiling strategy to track disease specific DNA methylation changes prevailing in 400 μl serum of lung cancer, fibrotic ILD and COPD patients. Plasma or serum samples, often referred to as ‘liquid biopsies’ have several advantages over tissue sampling: (a) they are easily accessible, (b) are not subject to biopsy bias and (c) can be repeatedly drawn from the same patient. The differential diagnosis attempt performed in the study on patients suffering from different lung diseases suggests that multiplexed cfDNA methylation profiling allows for the capture of these interconnected disease phenotypes, stabilizes the prediction and enhances diagnostic accuracy.
Collapse
Key Words
- AUC, area under curve
- Biomarker
- COPD, chronic obstructive pulmonary disease
- Ct-value, cycle threshold
- HOXD10
- HP, hypersensitivity pneumonitis
- ILD, interstitial lung disease, IPF, idiopathic pulmonary fibrosis
- Liquid biopsy
- MSP, methyl specific priming
- MSRE, methyl sensitive restriction enzyme
- NSIP, non-specific interstitial pneumonitis
- PAX9
- ROC, receiver operating characteristics
- UIP, usual interstitial pneumonia
- cfDNA, cell-free DNA
- methyl-sensitive restriction enzyme
- multiplex PCR
Collapse
Affiliation(s)
- Matthias Wielscher
- AIT - Austrian Institute of Technology, Health & Environment Department, Molecular Diagnostics Unit, Muthgasse 11/2, 1190 Vienna, Austria
| | - Klemens Vierlinger
- AIT - Austrian Institute of Technology, Health & Environment Department, Molecular Diagnostics Unit, Muthgasse 11/2, 1190 Vienna, Austria
| | - Ulrike Kegler
- AIT - Austrian Institute of Technology, Health & Environment Department, Molecular Diagnostics Unit, Muthgasse 11/2, 1190 Vienna, Austria
| | - Rolf Ziesche
- Medical University of Vienna, Clinical Department for Pulmonology, Spitalgasse 23, 1090 Vienna, Austria
| | - Andrea Gsur
- Medical University of Vienna, Institute of Cancer Research, Borschkegasse 8A, 1090 Vienna, Austria
| | - Andreas Weinhäusel
- AIT - Austrian Institute of Technology, Health & Environment Department, Molecular Diagnostics Unit, Muthgasse 11/2, 1190 Vienna, Austria
| |
Collapse
|
141
|
Castells A. Choosing the optimal method in programmatic colorectal cancer screening: current evidence and controversies. Therap Adv Gastroenterol 2015; 8:221-33. [PMID: 26136839 PMCID: PMC4480573 DOI: 10.1177/1756283x15578610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Colorectal cancer (CRC) is an important health problem all over the world, being the third most common cancer and the second leading cause of cancer-related death in Western countries. The most important strategy for CRC prevention is screening (i.e. secondary prevention). Since it is widely accepted that adenomas and serrated polyps are the precursors of the vast majority of CRC, early detection and removal of these lesions is associated with a reduction of CRC incidence and, consequently, mortality. Moreover, cancers detected by screening are usually diagnosed at early stages and, therefore, curable by endoscopic or surgical procedures. This review will be address CRC screening strategies in average-risk population, which is defined by those individuals, men and women, 50 years of age or older, without any additional personal or familial predisposing risk factor. In order to maximize the impact of screening and ensure high coverage and equity of access, only organized screening programs (i.e. programmatic screening) should be implemented, as opposed to case-finding or opportunistic screening. For that reason and considering that the optimal approach for colorectal screening may differ depending on the scenario, this review will be focused on the advantages and limitations of each screening strategy in an organized setting.
Collapse
Affiliation(s)
- Antoni Castells
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), IDIBAPS, University of Barcelona, Villarroel 170, 08036-Barcelona, Catalonia, Spain
| |
Collapse
|
142
|
Barault L, Amatu A, Bleeker FE, Moutinho C, Falcomatà C, Fiano V, Cassingena A, Siravegna G, Milione M, Cassoni P, De Braud F, Rudà R, Soffietti R, Venesio T, Bardelli A, Wesseling P, de Witt Hamer P, Pietrantonio F, Siena S, Esteller M, Sartore-Bianchi A, Di Nicolantonio F. Digital PCR quantification of MGMT methylation refines prediction of clinical benefit from alkylating agents in glioblastoma and metastatic colorectal cancer. Ann Oncol 2015; 26:1994-1999. [PMID: 26113646 DOI: 10.1093/annonc/mdv272] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/11/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND O(6)-methyl-guanine-methyl-transferase (MGMT) silencing by promoter methylation may identify cancer patients responding to the alkylating agents dacarbazine or temozolomide. PATIENTS AND METHODS We evaluated the prognostic and predictive value of MGMT methylation testing both in tumor and cell-free circulating DNA (cfDNA) from plasma samples using an ultra-sensitive two-step digital PCR technique (methyl-BEAMing). Results were compared with two established techniques, methylation-specific PCR (MSP) and Bs-pyrosequencing. RESULTS Thresholds for MGMT methylated status for each technique were established in a training set of 98 glioblastoma (GBM) patients. The prognostic and the predictive value of MGMT methylated status was validated in a second cohort of 66 GBM patients treated with temozolomide in which methyl-BEAMing displayed a better specificity than the other techniques. Cutoff values of MGMT methylation specific for metastatic colorectal cancer (mCRC) tissue samples were established in a cohort of 60 patients treated with dacarbazine. In mCRC, both quantitative assays methyl-BEAMing and Bs-pyrosequencing outperformed MSP, providing better prediction of treatment response and improvement in progression-free survival (PFS) (P < 0.001). Ability of methyl-BEAMing to identify responding patients was validated in a cohort of 23 mCRC patients treated with temozolomide and preselected for MGMT methylated status according to MSP. In mCRC patients treated with dacarbazine, exploratory analysis of cfDNA by methyl-BEAMing showed that MGMT methylation was associated with better response and improved median PFS (P = 0.008). CONCLUSIONS Methyl-BEAMing showed high reproducibility, specificity and sensitivity and was applicable to formalin-fixed paraffin-embedded tissues and cfDNA. This study supports the quantitative assessment of MGMT methylation for clinical purposes since it could refine prediction of response to alkylating agents.
Collapse
Affiliation(s)
- L Barault
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin)
| | - A Amatu
- Niguarda Cancer Center, Ospedale Niguarda Ca' Granda, Milan, Italy
| | - F E Bleeker
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - C Moutinho
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - C Falcomatà
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin)
| | - V Fiano
- Department of Medical Sciences, University of Turin, Città Della Salute e Della Scienza Hospital, Turin
| | - A Cassingena
- Niguarda Cancer Center, Ospedale Niguarda Ca' Granda, Milan, Italy
| | - G Siravegna
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin); Department of Oncology, University of Torino, Candiolo (Turin); FIRC Institute of Molecular Oncology (IFOM), Milan
| | - M Milione
- Departments of Pathology and Laboratory Medicine
| | - P Cassoni
- Department of Medical Sciences, University of Turin, Città Della Salute e Della Scienza Hospital, Turin
| | - F De Braud
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan
| | - R Rudà
- Department of Neuro-Oncology, University of Turin and Città Della Salute e Della Scienza Hospital, Turin, Italy
| | - R Soffietti
- Department of Neuro-Oncology, University of Turin and Città Della Salute e Della Scienza Hospital, Turin, Italy
| | - T Venesio
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin)
| | - A Bardelli
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin); Department of Oncology, University of Torino, Candiolo (Turin)
| | - P Wesseling
- Department of Pathology, VU University Medical Center, Amsterdam; Department of Pathology, Radboud University Medical Center, Nijmegen
| | - P de Witt Hamer
- Department Neurosurgery, Neurosurgical Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | | | - S Siena
- Niguarda Cancer Center, Ospedale Niguarda Ca' Granda, Milan, Italy
| | - M Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, Catalonia; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - F Di Nicolantonio
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin); Department of Oncology, University of Torino, Candiolo (Turin).
| |
Collapse
|
143
|
Colorectal Cancer Biomarkers: Where Are We Now? BIOMED RESEARCH INTERNATIONAL 2015; 2015:149014. [PMID: 26106599 PMCID: PMC4461726 DOI: 10.1155/2015/149014] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/19/2015] [Indexed: 12/18/2022]
Abstract
Colorectal cancer is one of the major causes of cancer-related death in the Western world. Patient survival is highly dependent on the tumor stage at the time of diagnosis. Reduced sensitivity to chemotherapy is still a major obstacle in effective treatment of advanced disease. Due to the fact that colorectal cancer is mostly asymptomatic until it progresses to advanced stages, the implementation of screening programs aimed at early detection is essential to reduce incidence and mortality rates. Current screening and diagnostic methods range from semi-invasive procedures such as colonoscopy to noninvasive stool-based tests. The combination of the absence of symptoms, the semi-invasive nature of currently used methods, and the suboptimal accuracy of fecal blood tests results in colorectal cancer diagnosis at advanced stages in a significant number of individuals. Alterations in gene expression leading to colorectal carcinogenesis are reflected in dysregulated levels of nucleic acids and proteins, which can be used for the development of novel, minimally invasive molecular biomarkers. The purpose of this review is to discuss the commercially available colorectal cancer molecular diagnostic methods as well as to highlight some of the new candidate predictive and prognostic molecular markers for tumor, stool, and blood samples.
Collapse
|
144
|
Warton K, Samimi G. Methylation of cell-free circulating DNA in the diagnosis of cancer. Front Mol Biosci 2015; 2:13. [PMID: 25988180 PMCID: PMC4428375 DOI: 10.3389/fmolb.2015.00013] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/07/2015] [Indexed: 01/04/2023] Open
Abstract
A range of molecular alterations found in tumor cells, such as DNA mutations and DNA methylation, is reflected in cell-free circulating DNA (circDNA) released from the tumor into the blood, thereby making circDNA an ideal candidate for the basis of a blood-based cancer diagnosis test. In many cancer types, mutations driving tumor development and progression are present in a wide range of oncogenes and tumor suppressor genes. However, even when a gene is consistently mutated in a particular cancer, the mutations can be spread over very large regions of its sequence, making evaluation difficult. This diversity of sequence changes in tumor DNA presents a challenge for the development of blood tests based on DNA mutations for cancer diagnosis. Unlike mutations, DNA methylation that can be consistently measured, as it tends to occur in specific regions of the DNA called CpG islands. Since DNA methylation is reflected within circDNA, detection of tumor-specific DNA methylation in patient plasma is a feasible approach for the development of a blood-based test. Aberrant circDNA methylation has been described in most cancer types and is actively being investigated for clinical applications. A commercial blood test for colorectal cancer based on the methylation of the SEPT9 promoter region in circDNA is under review for approval by the Federal Drug Administration (FDA) for clinical use. In this paper, we review the state of research in circDNA methylation as an application for blood-based diagnostic tests in colorectal, breast, lung, pancreatic and ovarian cancers, and we consider some of the future directions and challenges in this field. There are a number of potential circDNA biomarkers currently under investigation, and experience with SEPT9 shows that the time to clinical translation can be relatively rapid, supporting the promise of circDNA as a biomarker.
Collapse
Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Goli Samimi
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| |
Collapse
|
145
|
Head-to-head antisense transcription and R-loop formation promotes transcriptional activation. Proc Natl Acad Sci U S A 2015; 112:5785-90. [PMID: 25902512 DOI: 10.1073/pnas.1421197112] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The mechanisms used by antisense transcripts to regulate their corresponding sense mRNAs are not fully understood. Herein, we have addressed this issue for the vimentin (VIM) gene, a member of the intermediate filament family involved in cell and tissue integrity that is deregulated in different types of cancer. VIM mRNA levels are positively correlated with the expression of a previously uncharacterized head-to-head antisense transcript, both transcripts being silenced in colon primary tumors concomitant with promoter hypermethylation. Furthermore, antisense transcription promotes formation of an R-loop structure that can be disfavored in vitro and in vivo by ribonuclease H1 overexpression, resulting in VIM down-regulation. Antisense knockdown and R-loop destabilization both result in chromatin compaction around the VIM promoter and a reduction in the binding of transcriptional activators of the NF-κB pathway. These results are the first examples to our knowledge of R-loop-mediated enhancement of gene expression involving head-to-head antisense transcription at a cancer-related locus.
Collapse
|
146
|
Abstract
BACKGROUND Gastric cancer and colorectal cancer, the two most frequent cancers within the gastrointestinal tract, account for a large proportion of human malignancies worldwide. The initiation and progression of gastrointestinal cancer (GIC) is controlled by both genetic and epigenetic events. Epigenetic alterations, including changes in DNA methylation, specific histone modifications, chromatin remodeling and noncoding RNA-mediated gene silencing, are potentially reversible and heritable. SUMMARY In this article, we summarize the current advances in epigenetic biomarkers as potential substrates for GIC detection. The combined screening of a panel of methylated genes, hyperacetylated histones, microRNAs or other noncoding RNAs is currently under evaluation to improve sensitivity. KEY MESSAGE Current studies concentrated on the development of cost-effective epigenetic diagnostic biomarkers for GIC based on noninvasive blood or stool samples. The combined blood or stool test with a relatively high sensitivity could be a cost-effective screening tool for the detection of patients with asymptomatic cancers who could therefore choose whether or not to go for further examinations, such as endoscopy or colonoscopy. PRACTICAL IMPLICATIONS A better understanding of epigenetic mechanisms has not only offered new insights into a deeper understanding of the underlying mechanisms of carcinogenesis, but has also allowed identification of clinically relevant putative biomarkers for the early detection, disease monitoring, prognosis and risk assessment of GIC. In particular, noninvasive biomarkers in serum or fecal samples for the detection of GIC could have potential for better compliance and can be incorporated into routine clinical practice in the foreseeable future, pending their validation in large-scale prospective trials.
Collapse
Affiliation(s)
- Hui-Mi Chen
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai Institute of Digestive Disease, China ; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, China ; State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Jing-Yua Fang
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai Institute of Digestive Disease, China ; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, China ; State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| |
Collapse
|
147
|
Abstract
Many methods have been developed for DNA integrity assessment including electrophoresis-based procedures, quantitative PCR, and, more recently, microfluidics-based procedures. DNA integrity evaluation can be employed for characterizing biological samples quality before extensive genomic analysis and also finds applications in reproductive medicine, prenatal diagnostics, or cancer research. In this chapter, we will focus on the assessment of DNA integrity in cancer research. In particular, we will present the application of the determination of DNA integrity for tracking of circulating tumor DNA. Finally, we will conclude by illustrating the potential innovative application of DNA integrity as a biomarker in clinical research, especially for prognostic purposes, patient follow-up, or early diagnosis.
Collapse
|
148
|
Hudecova I. Digital PCR analysis of circulating nucleic acids. Clin Biochem 2015; 48:948-56. [PMID: 25828047 DOI: 10.1016/j.clinbiochem.2015.03.015] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 03/19/2015] [Indexed: 12/18/2022]
Abstract
Detection of plasma circulating nucleic acids (CNAs) requires the use of extremely sensitive and precise methods. The commonly used quantitative real-time polymerase chain reaction (PCR) poses certain technical limitations in relation to the precise measurement of CNAs whereas the costs of massively parallel sequencing are still relatively high. Digital PCR (dPCR) now represents an affordable and powerful single molecule counting strategy to detect minute amounts of genetic material with performance surpassing many quantitative methods. Microfluidic (chip) and emulsion (droplet)-based technologies have already been integrated into platforms offering hundreds to millions of nanoliter- or even picoliter-scale reaction partitions. The compelling observations reported in the field of cancer research, prenatal testing, transplantation medicine and virology support translation of this technology into routine use. Extremely sensitive plasma detection of rare mutations originating from tumor or placental cells among a large background of homologous sequences facilitates unraveling of the early stages of cancer or the detection of fetal mutations. Digital measurement of quantitative changes in plasma CNAs associated with cancer or graft rejection provides valuable information on the monitoring of disease burden or the recipient's immune response and subsequent therapy treatment. Furthermore, careful quantitative assessment of the viral load offers great value for effective monitoring of antiviral therapy for immunosuppressed or transplant patients. The present review describes the inherent features of dPCR that make it exceptionally robust in precise and sensitive quantification of CNAs. Moreover, I provide an insight into the types of potential clinical applications that have been developed by researchers to date.
Collapse
Affiliation(s)
- Irena Hudecova
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.
| |
Collapse
|
149
|
Caen O, Nizard P, Garrigou S, Perez-Toralla K, Zonta E, Laurent-Puig P, Taly V. PCR digitale en micro-compartiments. Med Sci (Paris) 2015; 31:180-6. [DOI: 10.1051/medsci/20153102015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
|
150
|
Bresalier RS, Kopetz S, Brenner DE. Blood-based tests for colorectal cancer screening: do they threaten the survival of the FIT test? Dig Dis Sci 2015; 60:664-71. [PMID: 25680874 DOI: 10.1007/s10620-015-3575-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 01/31/2015] [Indexed: 02/06/2023]
Abstract
Colorectal cancer is the second leading cause of cancer death in industrialized nations, accounting for 10% of the total cancer burden with an individual lifetime risk of ~6% in the USA (Siegel et al. in CA Cancer J Clin 62:9-29, 2014, American Cancer Society in Colorectal cancer facts and figures 2011-2013. American Cancer Society, Atlanta, 2011, Siegel et al. in CA Cancer J Clin 61:212-236, 2011). Although numerous screening methods have been incorporated into guidelines for colorectal cancer screening, no guideline includes a noninvasive blood-based test as a recommended option.
Collapse
Affiliation(s)
- Robert S Bresalier
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1466, Houston, TX, 77030, USA,
| | | | | |
Collapse
|