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Volovat SR, Augustin I, Zob D, Boboc D, Amurariti F, Volovat C, Stefanescu C, Stolniceanu CR, Ciocoiu M, Dumitras EA, Danciu M, Apostol DGC, Drug V, Shurbaji SA, Coca LG, Leon F, Iftene A, Herghelegiu PC. Use of Personalized Biomarkers in Metastatic Colorectal Cancer and the Impact of AI. Cancers (Basel) 2022; 14:cancers14194834. [PMID: 36230757 PMCID: PMC9562853 DOI: 10.3390/cancers14194834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/18/2022] [Accepted: 09/29/2022] [Indexed: 12/09/2022] Open
Abstract
Colorectal cancer is a major cause of cancer-related death worldwide and is correlated with genetic and epigenetic alterations in the colonic epithelium. Genetic changes play a major role in the pathophysiology of colorectal cancer through the development of gene mutations, but recent research has shown an important role for epigenetic alterations. In this review, we try to describe the current knowledge about epigenetic alterations, including DNA methylation and histone modifications, as well as the role of non-coding RNAs as epigenetic regulators and the prognostic and predictive biomarkers in metastatic colorectal disease that can allow increases in the effectiveness of treatments. Additionally, the intestinal microbiota’s composition can be an important biomarker for the response to strategies based on the immunotherapy of CRC. The identification of biomarkers in mCRC can be enhanced by developing artificial intelligence programs. We present the actual models that implement AI technology as a bridge connecting ncRNAs with tumors and conducted some experiments to improve the quality of the model used as well as the speed of the model that provides answers to users. In order to carry out this task, we implemented six algorithms: the naive Bayes classifier, the random forest classifier, the decision tree classifier, gradient boosted trees, logistic regression and SVM.
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Affiliation(s)
- Simona-Ruxandra Volovat
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Iolanda Augustin
- Department of Medical Oncology, AI.Trestioreanu Institute of Oncology, 022328 Bucharest, Romania
| | - Daniela Zob
- Department of Medical Oncology, AI.Trestioreanu Institute of Oncology, 022328 Bucharest, Romania
| | - Diana Boboc
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Florin Amurariti
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Constantin Volovat
- Department of Medical Oncology, “Euroclinic” Center of Oncology, 2 Vasile Conta Str., 700106 Iasi, Romania
- Correspondence: (C.V.); (C.S.)
| | - Cipriana Stefanescu
- Department of Biophysics and Medical Physics-Nuclear Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
- Correspondence: (C.V.); (C.S.)
| | - Cati Raluca Stolniceanu
- Department of Biophysics and Medical Physics-Nuclear Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Manuela Ciocoiu
- Department of Pathophysiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Eduard Alexandru Dumitras
- Department of Pathophysiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
- Department of Anesthesiology and Intensive Care, Regional Institute of Oncology, 700115 Iasi, Romania
| | - Mihai Danciu
- Pathology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | | | - Vasile Drug
- Department of Gastroenterology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
- Gastroenterology Clinic, Institute of Gastroenterology and Hepatology, ‘St. Spiridon’ Clinical Hospital, 700115 Iasi, Romania
| | - Sinziana Al Shurbaji
- Gastroenterology Clinic, Institute of Gastroenterology and Hepatology, ‘St. Spiridon’ Clinical Hospital, 700115 Iasi, Romania
| | - Lucia-Georgiana Coca
- Faculty of Computer Science, Alexandru Ioan Cuza University, 700115 Iasi, Romania
| | - Florin Leon
- Faculty of Automatic Control and Computer Engineering, Gheorghe Asachi Technical University, 700115 Iasi, Romania
| | - Adrian Iftene
- Faculty of Computer Science, Alexandru Ioan Cuza University, 700115 Iasi, Romania
| | - Paul-Corneliu Herghelegiu
- Faculty of Automatic Control and Computer Engineering, Gheorghe Asachi Technical University, 700115 Iasi, Romania
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Baksh M, Mahajan B, Dufresne MM, Shoukry MM, Nussbaum S, Abbaszadeh-Kasbi A, Ashary M, Vandenberg J, Gabriel EM. Circulating tumor DNA for breast cancer: Review of active clinical trials. Cancer Treat Res Commun 2022; 32:100609. [PMID: 35850075 DOI: 10.1016/j.ctarc.2022.100609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/17/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The new diagnostic concept of liquid biopsy is based on the analysis of circulating tumor cells (CTCs) and cell-free DNA (ctDNA). In addition to providing a more comprehensive view of the tumor characteristics including molecular variations, ctDNA analysis through liquid biopsies may also allow for a non-invasive, rapid, and cost-effective identification of biomarkers for tumor detection and monitoring of tumor progression. OBJECTIVE In this review, we summarize key active clinical trial studies involving utilization of ctDNA derived from liquid biopsy in the early and metastatic breast cancer setting. With this, we also provide a brief overview of the potential future implementations of the LB technology and outlining how ctDNA analysis needs to be standardized through the performance of similar clinical studies. METHODS A review was conducted on Clinicaltrials.gov to identify active trials related to use of circulating tumor DNA (ctDNA) for breast cancer. Search terms included "breast cancer," "liquid biopsy," and "ctDNA." CONCLUSION While LB is gaining traction in many cancer settings, its use in BC is still early and warrants more investigation in breast cancer diagnostic and treatment settings, including early detection of disease recurrence.
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Affiliation(s)
- Mizba Baksh
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America.
| | - Biraaj Mahajan
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Maria M Dufresne
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Mira M Shoukry
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Samuel Nussbaum
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Ali Abbaszadeh-Kasbi
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Mohammed Ashary
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Jonathan Vandenberg
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Emmanuel M Gabriel
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
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Saha S, Araf Y, Promon SK. Circulating tumor DNA in cancer diagnosis, monitoring, and prognosis. J Egypt Natl Canc Inst 2022; 34:8. [PMID: 35187602 DOI: 10.1186/s43046-022-00109-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/29/2022] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has become one of the crucial components for cancer detection with the increase of precision medicine practice. ctDNA has great potential as a blood-based biomarker for the detection and treatment of cancer in its early stages. The purpose of this article was to discuss ctDNA and how it can be utilized to detect cancer. The benefits and drawbacks of this cancer detection technology, as well as the field's future possibilities in various cancer management scenarios, are discussed. MAIN TEXT: ctDNA has clinical applications in disease diagnosis and monitoring. It can be used to identify mutations of interest and genetic heterogeneity. Another use of ctDNA is to monitor the effects of therapy by detecting mutation-driven resistance. Different technologies are being used for the detection of ctDNA. Next-generation sequencing, digital PCR, real-time PCR, and mass spectrometry are used. Using dPCR makes it possible to partition and analyze individual target sequences from a complex mixture. Mass-spectrometry technology enables accurate detection and quantification of ctDNA mutations at low frequency. Surface-enhanced Raman spectroscopy (SERS) and UltraSEEK are two systems based on this technology. There is no unified standard for detecting ctDNA as it exists in a low concentration in blood. As there is no defined approach, false positives occur in several methods due to inadequate sensitivities. Techniques used in ctDNA are costly and there is a limitation in clinical settings. SHORT CONCLUSION A detailed investigation is urgently needed to increase the test's accuracy and sensitivity. To find a standard marker for all forms of cancer DNA, more study is needed. Low concentrations of ctDNA in a sample require improved technology to provide the precision that low concentrations of ctDNA in a sample afford.
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Affiliation(s)
- Sudeepto Saha
- Department of Life Sciences, School of Environment and Life Sciences, Independent University, Bangladesh (IUB), Dhaka, Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
| | - Salman Khan Promon
- Department of Life Sciences, School of Environment and Life Sciences, Independent University, Bangladesh (IUB), Dhaka, Bangladesh.
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Broccard SP, Kasbi AA, Bagaria SP, Jones J, Shoudry M, Gabriel EM. Liquid biopsies for colorectal cancer: a narrative review of ongoing clinical trials and the current use of this technology at a comprehensive cancer center. J Gastrointest Oncol 2022; 13:438-449. [PMID: 35284120 PMCID: PMC8899730 DOI: 10.21037/jgo-21-470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/30/2021] [Indexed: 08/10/2023] Open
Abstract
OBJECTIVE In this review, we summarize ongoing clinical trials involving liquid biopsies (LB) for colorectal cancer (CRC), outlining the current landscape and the future implementation of this technology. We also describe the current use of LB in CRC treatment at our institution, the Mayo Clinic Enterprise. BACKGROUND The use of LB in CRC treatment merits close attention. Their role is being evaluated in the screening, non-intervention, intervention, and surveillance settings through many active trials. This, coupled with the technique's rapid integration into clinical practice, creates constant evolution of care. METHODS Review of ClinicalTrials.gov was performed identifying relevant and active trials involving LB for CRC. "Colorectal cancer" plus other terms including "liquid biopsies" and "ctDNA" were used as search terms, identifying 35 active trials. CONCLUSIONS LB use for the CRC is actively being investigated and requires close attention. Based on current evidence, Mayo Clinic Enterprise currently uses LB in the non-interventional, interventional and surveillance setting, but not for screening. Results of these trials may further establish the use of LB in the management of CRC.
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Affiliation(s)
| | | | | | - Jeremy Jones
- Division of Oncology, Mayo Clinic, Jacksonville, FL, USA
| | - Mira Shoudry
- Section of Surgical Oncology, Mayo Clinic, Jacksonville, FL, USA
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Applications of liquid biopsy in the Pharmacological Audit Trail for anticancer drug development. Nat Rev Clin Oncol 2021; 18:454-467. [PMID: 33762744 DOI: 10.1038/s41571-021-00489-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 02/06/2023]
Abstract
Anticancer drug development is a costly and protracted activity, and failure at late phases of clinical testing is common. We have previously proposed the Pharmacological Audit Trail (PhAT) intended to improve the efficiency of drug development, with a focus on the use of tumour tissue-based biomarkers. Blood-based 'liquid biopsy' approaches, such as targeted or whole-genome sequencing studies of plasma circulating cell-free tumour DNA (ctDNA) and circulating tumour cells (CTCs), are of increasing relevance to this drug development paradigm. Liquid biopsy assays can provide quantitative and qualitative data on prognostic, predictive, pharmacodynamic and clinical response biomarkers, and can also enable the characterization of disease evolution and resistance mechanisms. In this Perspective, we examine the promise of integrating liquid biopsy analyses into the PhAT, focusing on the current evidence, advances, limitations and challenges. We emphasize the continued importance of analytical validation and clinical qualification of circulating tumour biomarkers through prospective clinical trials.
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Laugsand EA, Brenne SS, Skorpen F. DNA methylation markers detected in blood, stool, urine, and tissue in colorectal cancer: a systematic review of paired samples. Int J Colorectal Dis 2021; 36:239-251. [PMID: 33030559 PMCID: PMC7801356 DOI: 10.1007/s00384-020-03757-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/17/2020] [Indexed: 02/04/2023]
Abstract
PURPOSE Methylated cell-free DNA in liquid biopsies are promising non-invasive biomarkers for colorectal cancer (CRC). Optimal markers would have high sensitivity and specificity for early detection of CRC and could be detected in more than one type of material from the patient. We systematically reviewed the literature on DNA methylation markers of colorectal cancer, detected in more than one type of material, regarding their potential as contributors to a panel for screening and follow-up of CRC. METHODS The databases MEDLINE, Web of Science, and Embase were systematically searched. Data extraction and review was performed by two authors independently. Agreement between methylation status in tissue and other materials (blood/stool/urine) was analyzed using the McNemar test and Cohen's kappa. RESULTS From the 51 included studies, we identified seven single markers with sensitivity ≥ 75% and specificity ≥ 90% for CRC. We also identified one promising plasma panel and two stool panels. The correspondence of methylation status was evaluated as very good for four markers, but only marginal for most of the other markers investigated (12 of 21). CONCLUSION The included studies reported only some of the variables and markers of interest and included few patients. Hence, a meta-analysis was not possible at this point. Larger, prospective studies must be designed to study the discordant detection of markers in tissue and liquid biopsies. When reporting their findings, such studies should use a standardized format.
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Affiliation(s)
- Eivor Alette Laugsand
- Department of Surgery, Levanger Hospital, Nord-Trøndelag Hospital trust, N-7600, Levanger, Norway.
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway.
| | - Siv Sellæg Brenne
- Department of Surgery, Levanger Hospital, Nord-Trøndelag Hospital trust, N-7600, Levanger, Norway
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway
| | - Frank Skorpen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway
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Steele JL, Stevens RC, Cabrera OA, Bassill GJ, Cramer SM, Guzman F, Shuber AP. Novel CRISPR-based sequence specific enrichment methods for target loci and single base mutations. PLoS One 2020; 15:e0243781. [PMID: 33362267 PMCID: PMC7757808 DOI: 10.1371/journal.pone.0243781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/25/2020] [Indexed: 01/10/2023] Open
Abstract
The programmable sequence specificity of CRISPR has found uses in gene editing and diagnostics. This manuscript describes an additional application of CRISPR through a family of novel DNA enrichment technologies. CAMP (CRISPR Associated Multiplexed PCR) and cCAMP (chimeric CRISPR Associated Multiplexed PCR) utilize the sequence specificity of the Cas9/sgRNA complex to target loci for the ligation of a universal adapter that is used for subsequent amplification. cTRACE (chimeric Targeting Rare Alleles with CRISPR-based Enrichment) also applies this method to use Cas9/sgRNA to target loci for the addition of universal adapters, however it has an additional selection for specific mutations through the use of an allele-specific primer. These three methods can produce multiplex PCR that significantly reduces the optimization required for every target. The methods are also not specific to any downstream analytical platform. We additionally will present a mutation specific enrichment technology that is non-amplification based and leaves the DNA in its native state: TRACE (Targeting Rare Alleles with CRISPR-based Enrichment). TRACE utilizes the Cas9/sgRNA complex to sterically protect the ends of targeted sequences from exonuclease activity which digests both the normal variant as well as any off-target sequences.
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Affiliation(s)
| | | | - Oscar A. Cabrera
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Gary J. Bassill
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Sabrina M. Cramer
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Felipe Guzman
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Anthony P. Shuber
- Genetics Research LLC, Waltham, Massachusetts, United States of America
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Sharma A, Sharma KL, Bansal C, Kumar A. Updates on "Cancer Genomics and Epigenomics". World J Clin Oncol 2020; 11:890-897. [PMID: 33312884 PMCID: PMC7701914 DOI: 10.5306/wjco.v11.i11.890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/03/2020] [Accepted: 08/01/2020] [Indexed: 02/06/2023] Open
Abstract
The field of "Cancer Genomics and Epigenomes" has been widely investigated for their involvement in cancer to understand the basic processes of different malignancies. The aggregation of genetic and epigenetic alterations also displays a wide range of heterogeneity making it quite necessary to develop personalized treatment strategies. The complex interplay between DNA methylation and chromatin dynamics in malignant cells is one of the major epigenetic mechanisms that lead to gene activation and repression. Hence, each tumor needs to be fully characterized to satisfy the ideas of personalized treatment strategies. The present article addresses various aspects of genome characterization methods and their potential role in the field of cancer genomics and epigenomics.
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Affiliation(s)
- Aarti Sharma
- Department of Surgical Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India
| | - Kiran Lata Sharma
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Cherry Bansal
- Department of Pathology, Era’s Medical College and Hospital, Lucknow 226003, India
| | - Ashok Kumar
- Department of Surgical Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India
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Ramesh N, Sei E, Tsai PC, Bai S, Zhao Y, Troncoso P, Corn PG, Logothetis C, Zurita AJ, Navin NE. Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing. Genome Biol 2020; 21:162. [PMID: 32631448 PMCID: PMC7336456 DOI: 10.1186/s13059-020-02045-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/13/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Investigating genome evolution in response to therapy is difficult in human tissue samples. To address this challenge, we develop an unbiased whole-genome plasma DNA sequencing approach that concurrently measures genomic copy number and exome mutations from archival cryostored plasma samples. This approach is applied to study longitudinal blood plasma samples from prostate cancer patients, where longitudinal tissue biopsies from the bone and other metastatic sites have been challenging to collect. RESULTS A molecular characterization of archival plasma DNA from 233 patients and genomic profiling of 101 patients identifies clinical correlations of aneuploid plasma DNA profiles with poor survival, increased plasma DNA concentrations, and lower plasma DNA size distributions. Deep-exome sequencing and genomic copy number profiling are performed on 23 patients, including 9 patients with matched metastatic tissues and 12 patients with serial plasma samples. These data show a high concordance in genomic alterations between the plasma DNA and metastatic tissue samples, suggesting the plasma DNA is highly representative of the tissue alterations. Longitudinal sequencing of 12 patients with 2-5 serial plasma samples reveals clonal dynamics and genome evolution in response to hormonal and chemotherapy. By performing an integrated evolutionary analysis, minor subclones are identified in 9 patients that expanded in response to therapy and harbored mutations associated with resistance. CONCLUSIONS This study provides an unbiased evolutionary approach to non-invasively delineate clonal dynamics and identify clones with mutations associated with resistance in prostate cancer.
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Affiliation(s)
- Naveen Ramesh
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX USA
| | - Emi Sei
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Pei Ching Tsai
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Shanshan Bai
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Yuehui Zhao
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Patricia Troncoso
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Paul G. Corn
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Amado J. Zurita
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Nicholas E. Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX USA
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
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Ran R, Huang W, Liu Y, Shao L, Liu X, Niu Y, Kong W, Bo S, Rugo HS, Lu S, Li H. Prognostic Value of Plasma HER2 Gene Copy Number in HER2-Positive Metastatic Breast Cancer Treated with First-Line Trastuzumab. Onco Targets Ther 2020; 13:4385-4395. [PMID: 32547071 PMCID: PMC7245474 DOI: 10.2147/ott.s240990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/24/2020] [Indexed: 12/30/2022] Open
Abstract
Objective Patients with HER2-positive metastatic breast cancer (MBC) benefit from trastuzumab-based therapy but eventually develop intrinsic or acquired resistance. Whether plasma HER2 gene copy number (GCN) could predict survival after trastuzumab treatment remained controversial. We evaluated the prognostic value of plasma HER2 GCN using low-coverage whole-genome sequencing (LC-WGS). Methods The plasma was collected from HER2-positive MBC patients whose pre-therapeutic samples were available before first-line trastuzumab-based treatment. Plasma DNA was extracted and assessed by LC-WGS for HER2 GCN. The optimal cut-off point for HER2 GCN to shorter survival was determined by receiver operating characteristic (ROC) curve analysis. Results A total of 49 patients were retrieved from 2013 to 2017, among whom 21 had multiple organ involvement (≥3 sites). Variations of HER2 GCN in pre-therapeutic plasma ranged from 1.89 to 23.86 (median = 2.59). ROC analysis identified the optimal cut-off point for HER2 GCN as 2.82 (P = 0.005), with 23 patients had high-level HER2 GCN and 26 in the low-level group. Both progression-free survival (PFS, P = 0.032) and overall survival (OS, P = 0.006) were adversely associated with high-level HER2 GCN. In multivariate analyses, high HER2 GCN was independently associated with shorter PFS [hazard ratio (HR) = 2.042, P = 0.037], while both high HER2 GCN (HR = 4.909, P = 0.004) and more metastatic organs (HR = 4.019, P = 0.011) were negative prognostic factors for OS. Conclusion In this population of patients with HER2-positive MBC, individuals with high HER2 GCNs in plasma had worse prognosis after trastuzumab-based therapy. Plasma HER2 GCN may be a prognostic marker in these patients.
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Affiliation(s)
- Ran Ran
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
| | - Wenfa Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
| | - Yaxin Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
| | - Lin Shao
- Department of Clinical Research, Yikon Genomics Co. Ltd., Shanghai, People's Republic of China
| | - Xiaoran Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
| | - Yunyun Niu
- Department of Clinical Research, Yikon Genomics Co. Ltd., Shanghai, People's Republic of China
| | - Weiyao Kong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
| | - Shiping Bo
- Department of Clinical Research, Yikon Genomics Co. Ltd., Shanghai, People's Republic of China
| | - Hope S Rugo
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Sijia Lu
- Department of Clinical Research, Yikon Genomics Co. Ltd., Shanghai, People's Republic of China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
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Max Ma X, Bendell JC, Hurwitz HI, Ju C, Lee JJ, Lovejoy A, Mancao C, Nicholas A, Price R, Sommer N, Tikoo N, Yao L, Yaung SJ, Palma JF. Disease Monitoring Using Post-induction Circulating Tumor DNA Analysis Following First-Line Therapy in Patients with Metastatic Colorectal Cancer. Clin Cancer Res 2020; 26:4010-4017. [PMID: 32220893 DOI: 10.1158/1078-0432.ccr-19-1209] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 11/22/2019] [Accepted: 03/23/2020] [Indexed: 12/22/2022]
Abstract
PURPOSE We assessed plasma circulating tumor DNA (ctDNA) level as a prognostic marker for progression-free survival (PFS) following first-line metastatic colorectal cancer (mCRC) therapy. EXPERIMENTAL DESIGN The Sequencing Triplet With Avastin and Maintenance (STEAM) was a randomized, phase II trial investigating efficacy of bevacizumab (BEV) plus 5-fluorouracil/leucovorin/oxaliplatin (FOLFOX) and 5-fluorouracil/leucovorin/irinotecan (FOLFIRI), administered concurrently or sequentially, versus FOLFOX-BEV in first-line mCRC. Evaluation of biomarkers associated with treatment outcomes was an exploratory endpoint. Patients in the biomarker-evaluable population (BEP) had 1 tissue sample, 1 pre-induction plasma sample, and 1 post-induction plasma sample collected ≤60 days of induction from last drug date. RESULTS Among the 280 patients enrolled in STEAM, 183 had sequenced and evaluable tumor tissue, 118 had matched pre-induction plasma, and 54 (BEP) had ctDNA-evaluable sequencing data for pre- and post-induction plasma. The most common somatic variants in tumor tissue and pre-induction plasma were TP53, APC, and KRAS. Patients with lower-than-median versus higher-than-median post-induction mean allele fraction (mAF) levels had longer median PFS (17.7 vs. 7.5 months, HR, 0.33; 95% confidence interval, 0.17-0.63). Higher levels of post-induction mAF and post-induction mean mutant molecules per milliliter (mMMPM), and changes in ctDNA (stratified by a 10-fold or 100-fold reduction in mAF between pre- and post-induction plasma), were associated with shorter PFS. Post-induction mAF and mMMPM generally correlated with each other (ρ = 0.987, P < 0.0001). CONCLUSIONS ctDNA quantification in post-induction plasma may serve as a prognostic biomarker for mCRC post-treatment outcomes.
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Affiliation(s)
- Xiaoju Max Ma
- Medical Scientific Affairs, Roche Sequencing Solutions, Inc., Pleasanton, California.
| | - Johanna C Bendell
- Drug Development Unit, Sarah Cannon Research Institute/Tennessee Oncology, Nashville, Tennessee
| | - Herbert I Hurwitz
- Project Development Oncology, Genentech, Inc., South San Francisco, California
| | - Christine Ju
- Clinical Operations and Biometrics, Roche Molecular Systems, Pleasanton, California
| | - John J Lee
- Medical Scientific Affairs, Roche Sequencing Solutions, Inc., Pleasanton, California
| | - Alex Lovejoy
- Assay Development, Roche Sequencing Solutions, Inc., Pleasanton, California
| | - Christoph Mancao
- Oncology Biomarker Development, Genentech, Inc., Basel, Switzerland
| | - Alan Nicholas
- US Medical Affairs and Biometrics, Genentech, Inc., South San Francisco, California
| | - Richard Price
- Oncology Biomarker Development, Genentech, Inc., Basel, Switzerland
| | - Nicolas Sommer
- Medical Affairs BioOncology, Genentech, Inc., South San Francisco, California
| | - Nalin Tikoo
- Clinical Operations and Biometrics, Roche Molecular Systems, Pleasanton, California
| | - Lijing Yao
- Bioinformatics Research and Early Development, Roche Sequencing Solutions, Inc., Pleasanton, California
| | - Stephanie J Yaung
- Medical and Scientific Affairs Bioinformatics, Roche Sequencing Solutions, Inc., Pleasanton, California
| | - John F Palma
- Medical Scientific Affairs, Roche Sequencing Solutions, Inc., Pleasanton, California.
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12
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He Y, Ma X, Chen K, Liu F, Cai S, Han-Zhang H, Hou T, Xiang J, Peng J. Perioperative Circulating Tumor DNA in Colorectal Liver Metastases: Concordance with Metastatic Tissue and Predictive Value for Tumor Burden and Prognosis. Cancer Manag Res 2020; 12:1621-1630. [PMID: 32184665 PMCID: PMC7061429 DOI: 10.2147/cmar.s240869] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/08/2020] [Indexed: 12/18/2022] Open
Abstract
Background The surgical resection of colorectal cancer with liver metastases (CLM) has proven to be the most important modality for long-term survival, while effective biomarkers for outcome prediction or postoperative surveillance are still lacking. Currently, circulating biomarkers obtained from a liquid biopsy are widely used to assess the treatment response, disease recurrence and progression. In this study, we analyzed the value of the liquid biopsy, which includes circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA), in patients with CLM. Methods Capture-based targeted deep sequencing was performed on matched pre-surgery, post-surgery and liver metastatic tissues of 20 CRC patients who underwent the resection of liver metastases between May and September 2017 using a panel consisting of 41 genes. Mutation landscapes obtained from pre-surgery plasma samples and metastatic tissue samples were compared. Results Collectively, we identified 47 mutations from 17 pre-surgery plasma samples (85%), and the remaining 3 patients had no mutation detected from the panel. We revealed a high by-variant concordance rate of 82.14% between pre-surgery plasma samples and liver metastatic tissue samples. We further analyzed the correlation between ctDNA, cfDNA, CEA and tumor burden and revealed a positive correlation between ctDNA and tumor burden (R=0.69, p=0.002). As of the date for data cutoff, 8/20 patients experienced relapse. Our study also demonstrated that pre-surgery ctDNA (p<0.001), cfDNA (p=0.001) and CEA (p=0.012) levels had predictive value for relapse. Patients with low pre-surgery ctDNA (p<0.001), cfDNA (p=0.001) or CEA (p=0.012) levels were more likely to experience prolonged progression-free survival. Conclusion Our data demonstrate that the genomic profile obtained from ctDNA is comparable with the genomic profile obtained from metastatic liver tumors. Furthermore, our study also show that pre-surgery ctDNA levels are positively correlated with tumor burden. In addition, pre-surgery ctDNA, cfDNA and CEA levels have predictive value for relapse.
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Affiliation(s)
- Yiping He
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Xiaoji Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Ke Chen
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China.,Department of Endoscopy, Fudan University Shanghai Cancer Center, Shanghai 200032, People's Republic of China
| | - Fangqi Liu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Sanjun Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Han Han-Zhang
- Burning Rock Biotech, Guangzhou, Guangdong, People's Republic of China
| | - Ting Hou
- Burning Rock Biotech, Guangzhou, Guangdong, People's Republic of China
| | - Jianxing Xiang
- Burning Rock Biotech, Guangzhou, Guangdong, People's Republic of China
| | - Junjie Peng
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
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13
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Bender U, Rho YS, Barrera I, Aghajanyan S, Acoba J, Kavan P. Adjuvant therapy for stages II and III colon cancer: risk stratification, treatment duration, and future directions. Curr Oncol 2019; 26:S43-S52. [PMID: 31819709 PMCID: PMC6878933 DOI: 10.3747/co.26.5605] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background To date, the role of adjuvant systemic therapy in stages ii and iii colon cancer remains a topic of interest and debate. The objective of the present review was to assess the most recent data, specifically addressing methods of risk stratification, duration of therapy, and future directions. Methods PubMed and medline were searched for literature pertinent to adjuvant chemotherapy in either stage ii or stage iii colorectal cancer. Summary Locoregional disease, histopathology, age, laterality, and a number of other biologic and molecular markers appear to have a role in disease risk stratification. The duration of adjuvant therapy for stage iii disease can vary based on risk factors, but use of adjuvant therapy and duration of therapy in stage ii disease remain controversial. Future directions should include genomic assays and improved study design to provide concrete evidence about the duration of adjuvant folfox or capox and about other types of chemotherapy and immunotherapy.
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Affiliation(s)
- U Bender
- Gerald Bronfman Department of Oncology, McGill University Faculty of Medicine, Montreal, QC
| | - Y S Rho
- University of Hawaii Internal Medicine Program, Honolulu, HI, U.S.A
| | - I Barrera
- Gerald Bronfman Department of Oncology, McGill University Faculty of Medicine, Montreal, QC
| | - S Aghajanyan
- Gerald Bronfman Department of Oncology, McGill University Faculty of Medicine, Montreal, QC
| | - J Acoba
- University of Hawaii Internal Medicine Program, Honolulu, HI, U.S.A
- University of Hawaii Cancer Center, Honolulu, HI, U.S.A
| | - P Kavan
- Gerald Bronfman Department of Oncology, McGill University Faculty of Medicine, Montreal, QC
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14
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Diagnostic and Prognostic Value of B4GALT1 Hypermethylation and Its Clinical Significance as a Novel Circulating Cell-Free DNA Biomarker in Colorectal Cancer. Cancers (Basel) 2019; 11:cancers11101598. [PMID: 31635093 PMCID: PMC6826707 DOI: 10.3390/cancers11101598] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/10/2019] [Accepted: 10/17/2019] [Indexed: 12/24/2022] Open
Abstract
Epigenetic modifications of glyco-genes have been documented in different types of cancer and are tightly linked to proliferation, invasiveness, metastasis, and drug resistance. This study aims to investigate the diagnostic, prognostic, and therapy-response predictive value of the glyco-gene B4GALT1 in colorectal cancer (CRC) patients. A Kaplan–Meier analysis was conducted in 1418 CRC patients (GEO and TCGA datasets) to assess the prognostic and therapy-response predictive values of the aberrant expression and methylation status of B4GALT1. Quantitative methylation-specific PCR (QMSP) and droplet digital quantitative methylation-specific PCR (dd-QMSP) were respectively used to detect hypermethylated B4GALT1 in metastasis and plasma in four cohorts of metastatic CRC cases (mCRC). Both the downregulated expression and promoter hypermethylation of B4GALT1 have a negative prognostic impact on CRC. Interestingly a low expression level of B4GALT1 was significantly associated with poor cetuximab response (progression-free survival (PFS) p = 0.01) particularly in wild-type (WT)-KRAS patients (p = 0.03). B4GALT1 promoter was aberrantly methylated in liver and lung metastases. The detection of hypermethylated B4GALT1 in plasma of mCRC patients showed a highly discriminative receiver operating characteristic (ROC) curve profile (area under curve (AUC) value 0.750; 95% CI: 0.592–0.908, p = 0.008), clearly distinguishing mCRC patients from healthy controls. Based on an optimal cut-off value defined by the ROC analysis, B4GALT1 yield a 100% specificity and a 50% sensitivity. These data support the potential value of B4GALT1 as an additional novel biomarker for the prediction of cetuximab response, and as a specific and sensitive diagnostic circulating biomarker that can be detected in CRC.
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15
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Tuaeva NO, Falzone L, Porozov YB, Nosyrev AE, Trukhan VM, Kovatsi L, Spandidos DA, Drakoulis N, Kalogeraki A, Mamoulakis C, Tzanakakis G, Libra M, Tsatsakis A. Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements. Cells 2019; 8:E1251. [PMID: 31615102 PMCID: PMC6829588 DOI: 10.3390/cells8101251] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/30/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023] Open
Abstract
In recent years, the introduction of new molecular techniques in experimental and clinical settings has allowed researchers and clinicians to propose circulating-tumor DNA (ctDNA) analysis and liquid biopsy as novel promising strategies for the early diagnosis of cancer and for the definition of patients' prognosis. It was widely demonstrated that through the non-invasive analysis of ctDNA, it is possible to identify and characterize the mutational status of tumors while avoiding invasive diagnostic strategies. Although a number of studies on ctDNA in patients' samples significantly contributed to the improvement of oncology practice, some investigations generated conflicting data about the diagnostic and prognostic significance of ctDNA. Hence, to highlight the relevant achievements obtained so far in this field, a clearer description of the current methodologies used, as well as the obtained results, are strongly needed. On these bases, this review discusses the most relevant studies on ctDNA analysis in cancer, as well as the future directions and applications of liquid biopsy. In particular, special attention was paid to the early diagnosis of primary cancer, to the diagnosis of tumors with an unknown primary location, and finally to the prognosis of cancer patients. Furthermore, the current limitations of ctDNA-based approaches and possible strategies to overcome these limitations are presented.
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Affiliation(s)
- Natalia O Tuaeva
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Luca Falzone
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Naples, Italy.
| | - Yuri B Porozov
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- ITMO University, Saint Petersburg 197101, Russia.
| | - Alexander E Nosyrev
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Vladimir M Trukhan
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54248 Thessaloniki, Greece.
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Zografou, Greece.
| | - Alexandra Kalogeraki
- Department of Pathology-Cytopathology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, University of Crete, Medical School, Heraklion, 70013 Crete, Greece.
| | - George Tzanakakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Massimo Libra
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy.
| | - Aristides Tsatsakis
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, Heraklion, 71003 Crete, Greece.
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16
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Zhang L, Liang Y, Li S, Zeng F, Meng Y, Chen Z, Liu S, Tao Y, Yu F. The interplay of circulating tumor DNA and chromatin modification, therapeutic resistance, and metastasis. Mol Cancer 2019; 18:36. [PMID: 30849971 PMCID: PMC6408771 DOI: 10.1186/s12943-019-0989-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/26/2019] [Indexed: 02/07/2023] Open
Abstract
Peripheral circulating free DNA (cfDNA) is DNA that is detected in plasma or serum fluid with a cell-free status. For cancer patients, cfDNA not only originates from apoptotic cells but also from necrotic tumor cells and disseminated tumor cells that have escaped into the blood during epithelial-mesenchymal transition. Additionally, cfDNA derived from tumors, also known as circulating tumor DNA (ctDNA), carries tumor-associated genetic and epigenetic changes in cancer patients, which makes ctDNA a potential biomarker for the early diagnosis of tumors, monitory and therapeutic evaluations, and prognostic assessments, among others, for various kinds of cancer. Moreover, analyses of cfDNA chromatin modifications can reflect the heterogeneity of tumors and have potential for predicting tumor drug resistance.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Yiyi Liang
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Shifu Li
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Fanyuan Zeng
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Yongan Meng
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Ziwei Chen
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Yongguang Tao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China.
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China.
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China.
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.
| | - Fenglei Yu
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.
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17
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Advantage of Next-Generation Sequencing in Dynamic Monitoring of Circulating Tumor DNA over Droplet Digital PCR in Cetuximab Treated Colorectal Cancer Patients. Transl Oncol 2018; 12:426-431. [PMID: 30562681 PMCID: PMC6297189 DOI: 10.1016/j.tranon.2018.11.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 12/24/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) blockade resistance is common in the treatment of RAS wide type colorectal cancer (CRC). During the treatment of cetuximab, acquired resistant genomic alterations always occurs earlier than disease progression observed by medical images. Identification of genomic alterations dynamically might have certain clinical significance. Because of the limitation of repeated tissue biopsy, liquid biopsy is increasingly recognized. Droplet digital polymerase chain reaction (ddPCR) is the main detection methods for circulating tumor DNA (ctDNA), however, the application of next-generation sequencing (NGS) for ctDNA detection becomes more and more popular. Here we develop a NGS-based ctDNA assay and evaluated its sensitivity and specificity while using ddPCR as control. These two technologies were both used for genomic alteration detection for the peripheral blood samples from cetuximab-treated colorectal cancer patients dynamically. Fifteen patients were enrolled in this study, including eight males and seven females. The sensitivity and specificity of our NGS assay were 87.5% and 100% respectively, and liner regression analysis comparing variant allele frequency (VAF) revealed high concordance between NGS and ddPCR (R2 = 0.98). NGS actually found more mutation information than ddPCR such as the additional dynamic changes of TP53 which were observed in the disease progression patients. Moreover, the variant allele fraction of TP53 was also found by NGS to be changed along with the clinical efficacy evaluation dynamically during the whole treatment process. In conclusion, our newly developed NGS-based ctDNA assay shows similar performance with ddPCR but have more advantages of its high throughput of multigenetic detection for the dynamic monitoring during the treatment of cetuximab in metastasis CRC patients.
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