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Igder S, Zamani M, Fakher S, Siri M, Ashktorab H, Azarpira N, Mokarram P. Circulating Nucleic Acids in Colorectal Cancer: Diagnostic and Prognostic Value. DISEASE MARKERS 2024; 2024:9943412. [PMID: 38380073 PMCID: PMC10878755 DOI: 10.1155/2024/9943412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/07/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in the world and the fourth leading cause of cancer-related mortality. DNA (cfDNA/ctDNA) and RNA (cfRNA/ctRNA) in the blood are promising noninvasive biomarkers for molecular profiling, screening, diagnosis, treatment management, and prognosis of CRC. Technological advancements that enable precise detection of both genetic and epigenetic abnormalities, even in minute quantities in circulation, can overcome some of these challenges. This review focuses on testing for circulating nucleic acids in the circulation as a noninvasive method for CRC detection, monitoring, detection of minimal residual disease, and patient management. In addition, the benefits and drawbacks of various diagnostic techniques and associated bioinformatics tools have been detailed.
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Affiliation(s)
- Somayeh Igder
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Fakher
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Negar Azarpira
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
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Yamamoto M, Shindo M, Funayama T, Sumi C, Saito T, Toki Y, Hatayama M, Ono Y, Sato K, Mizukami Y, Okumura T. Monitoring mutant KRAS in plasma cell-free DNA can predict disease progression in a patient with multiple myeloma: A case report. Clin Chim Acta 2023; 551:117590. [PMID: 37837907 DOI: 10.1016/j.cca.2023.117590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/27/2023] [Accepted: 10/08/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND AND AIMS Multiple myeloma (MM), a neoplasm of plasma cells (PCs), is a highly heterogeneous disease with multifocal dissemination throughout the body. Minimal residual disease (MRD) detected using PCs in bone marrow (BM) is important for MM management; however, frequent invasive examinations impose a significant burden on patients. METHODS Analysis using plasma cell-free DNA (cfDNA) might represent an alternative tool for disease monitoring. In this study, we observed the disease status in a patient with MM by examining the KRAS mutation allele frequency (MAF) in plasma cfDNA using digital PCR. RESULTS During treatment, the MAF was correlated with serum immunoglobulin A and free light chain-kappa levels. After the second autologous peripheral blood stem cell transplantation, the KRAS MAF became immediately positive after confirming MRD negativity using PCs from BM. Shortly thereafter, the patient experienced clinical relapse primarily involving bone lesions. CONCLUSION Mutant KRAS monitoring in cfDNA using serial blood collection might reflect the disease status more accurately than invasive BM examinations, especially in patients with MM whose primary lesions have extra-BM locations. It could also help predict treatment responses and outcomes.
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Affiliation(s)
- Masayo Yamamoto
- Division of Metabolism and Biosystemic Science, Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan.
| | - Motohiro Shindo
- Division of Metabolism and Biosystemic Science, Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Takuya Funayama
- Division of Metabolism and Biosystemic Science, Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Chihiro Sumi
- Division of Metabolism and Biosystemic Science, Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Takeshi Saito
- Division of Metabolism and Biosystemic Science, Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Yasumichi Toki
- Division of Metabolism and Biosystemic Science, Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Mayumi Hatayama
- Division of Metabolism and Biosystemic Science, Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Kazuya Sato
- Department of Hematology/Oncology, Asahikawa Kosei Hospital, Asahikawa, Japan
| | - Yusuke Mizukami
- Division of Metabolism and Biosystemic Science, Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan; Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Toshikatsu Okumura
- Division of Metabolism and Biosystemic Science, Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
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3
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Takahashi K, Takeda Y, Ono Y, Isomoto H, Mizukami Y. Current status of molecular diagnostic approaches using liquid biopsy. J Gastroenterol 2023; 58:834-847. [PMID: 37470859 PMCID: PMC10423147 DOI: 10.1007/s00535-023-02024-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/08/2023] [Indexed: 07/21/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal cancers, and developing an efficient and reliable approach for its early-stage diagnosis is urgently needed. Precancerous lesions of PDAC, such as pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasms (IPMN), arise through multiple steps of driver gene alterations in KRAS, TP53, CDKN2A, SMAD4, or GNAS. Hallmark mutations play a role in tumor initiation and progression, and their detection in bodily fluids is crucial for diagnosis. Recently, liquid biopsy has gained attention as an approach to complement pathological diagnosis, and in addition to mutation signatures in cell-free DNA, cell-free RNA, and extracellular vesicles have been investigated as potential diagnostic and prognostic markers. Integrating such molecular information to revise the diagnostic criteria for pancreatic cancer can enable a better understanding of the pathogenesis underlying inter-patient heterogeneity, such as sensitivity to chemotherapy and disease outcomes. This review discusses the current diagnostic approaches and clinical applications of genetic analysis in pancreatic cancer and diagnostic attempts by liquid biopsy and molecular analyses using pancreatic juice, duodenal fluid, and blood samples. Emerging knowledge in the rapidly advancing liquid biopsy field is promising for molecular profiling and diagnosing pancreatic diseases with significant diversity.
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Affiliation(s)
- Kenji Takahashi
- Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Yohei Takeda
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Yusuke Ono
- Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Hajime Isomoto
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Yusuke Mizukami
- Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
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4
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Wang Y, Chu X, Chen X, Yin A, Yao Y, Wang L, Xu H, Liu F, Chen K, Wu Y. Non-invasive prenatal testing for fetal Ss, Kidd, and CTL2 blood group prediction by multiplex digital droplet PCR. Ther Adv Hematol 2023; 14:20406207231179334. [PMID: 37575175 PMCID: PMC10422893 DOI: 10.1177/20406207231179334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 05/15/2023] [Indexed: 08/15/2023] Open
Abstract
Background Some blood groups, such as S and s blood groups in the MNS blood group system, and Kidd and CTL2 blood group systems, can cause severe fetal and newborn alloimmune disorders. Non-invasive prenatal testing (NIPT) to predict fetal blood groups and knowledge of local blood group gene frequency are both important for pregnancy management decisions. Droplet digital PCR (ddPCR) has high specificity and sensitivity in detecting fetal single nucleotide variation. Objectives The objective is to predict fetal Ss, Kidd, and CTL2 blood groups using multiplex ddPCR. The gene frequencies of three blood groups were detected by ddPCR in northwest China. Design This is a prospective study. Methods Cell-free fetal DNA isolated from 26 healthy single pregnant women at different gestational stages was tested with QX200 Droplet Digital PCR. Results were compared with fetal genotypes. DNA samples purified from 20 blood pools containing a total of 1000 donors in northwest China were subjected to ddPCR to detect the gene frequency of three blood groups. Results Ss, Kidd, and CTL2 blood groups of 26 pregnant fetuses were accurately detected by multiplex ddPCR. The multiplex ddPCR results were consistent with the Sanger sequencing results of 26 fetal blood samples after birth. The gene frequencies of the three blood groups detected by ddPCR were 9.30% for S, 90.70% for s, 48.43% for Jka, 51.57% for Jkb, 66.57% for HNA-3A, and 33.43% for HNA-3B. Conclusions It is reliable to predict fetal Ss, Kidd, and CTL2 blood groups by multiplex ddPCR. Meanwhile, we designed a simple and efficient method for inferring the gene frequency of three blood groups based on ddPCR.
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Affiliation(s)
- Yufeng Wang
- Medical Research and Experiment Center, Medical College of Yan’an University, Yan’an University, Yan’an, P.R. China
| | - Xiaoyue Chu
- Blood Group Reference Laboratory, Shaanxi Institute of Blood Transfusion, Shaanxi Blood Center, Xi’an, P.R. China
| | - Xihui Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi’an, P.R. China
| | - Anan Yin
- Department of Neurosurgery, Xijing Institute of Clinical Neuroscience and Department of Plastic surgery, Xijing Hospital, Air Force Medical University, Xi’an, P.R. China
| | - Yan Yao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi’an, P.R. China
| | - Li Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi’an, P.R. China
- School of Aerospace Medicine, Air Force Medical University, Xi’an, P.R. China*These authors contributed equally to this work
| | | | - Fangfang Liu
- Department of Neurobiology, School of Basic Medicine, Air Force Medical University, Xi’an 710032, Shaanxi, P.R. China
| | - Kun Chen
- Department of Anatomy, Histology and Embryology and K.K. Leung Brain Research Centre, School of Basic Medicine, Air Force Medical University, Xi’an 710032, Shaanxi, P.R. China
| | - Yuanming Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi’an 710032, Shaanxi, P.R. China
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5
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Chiho M, Ono Y, Hayashi A, Takahashi K, Taniue K, Kakisaka R, Mori M, Ishii T, Sato H, Okada T, Kawabata H, Goto T, Tamamura N, Omori Y, Takahashi K, Katanuma A, Karasaki H, Liss AS, Mizukami Y. Multiplex digital PCR assay to detect multiple KRAS and GNAS mutations associated with pancreatic carcinogenesis from minimal specimen amounts. J Mol Diagn 2023; 25:367-377. [PMID: 36965665 DOI: 10.1016/j.jmoldx.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/27/2023] Open
Abstract
Digital PCR (dPCR) allows for highly sensitive quantification of low-frequency mutations and facilitates early detection of cancer. However, low throughput targeting of single hotspots in dPCR hinders variant specification when multiple probes are used. Here we developed a dPCR method to simultaneously identify major variants related to pancreatic carcinogenesis. Using a 2-D plot of droplet fluorescence under the optimized concentration of two fluorescent probe pools, we determined the absolute quantification of different KRAS and GNAS variants. Successful detection of the multiple driver mutations was verified in 24 surgically resected tumor samples from 19 patients and 22 FNA samples from patients with pancreatic ductal adenocarcinoma. Precise quantification of the variant allele frequency was optimized using template DNA at a concentration as low as 1-10 ng. Furthermore, amplicons targeting multiple hotspots were successfully enriched with fewer false positives using high-fidelity polymerase, allowing for the detection of various KRAS and GNAS mutations with high probability in small cell/tissue specimens. Using this target enrichment, mutations at a rate of 90% in small residual tissues, such as the FNA needle flush and microscopic lesions in resected specimens, have successfully been identified. The proposed method allows for low-cost and accurate detection of driver mutations to diagnose cancers, even with minimal tissue collection.
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Affiliation(s)
- Maeda Chiho
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan.
| | - Akihiro Hayashi
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Kenji Takahashi
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Kenzui Taniue
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan; Isotope Science Center, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Rika Kakisaka
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Miyuki Mori
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Takahiro Ishii
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Hiroki Sato
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan; Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Tetsuhiro Okada
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Hidemasa Kawabata
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Takuma Goto
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Nobue Tamamura
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Yuko Omori
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Kuniyuki Takahashi
- Center for Gastroenterology, Teine Keijinkai Hospital, Sapporo, 006-0811, Japan
| | - Akio Katanuma
- Center for Gastroenterology, Teine Keijinkai Hospital, Sapporo, 006-0811, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Andrew Scott Liss
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
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6
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Takano S, Fukasawa M, Enomoto N. Molecular assessment of endoscopically collected pancreatic juice and duodenal fluid from patients with pancreatic diseases. Dig Endosc 2023; 35:19-32. [PMID: 35665966 DOI: 10.1111/den.14371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/01/2022] [Indexed: 01/17/2023]
Abstract
One concern associated with pancreatic diseases is the poor prognosis of pancreatic cancer. Even with advances in diagnostic modalities, risk stratification of premalignant lesions and differentiation of pancreatic cysts are challenging. Pancreatic lesions of concern include intraductal papillary mucinous neoplasms, mucinous cystic neoplasms, serous cystadenomas, pseudocysts, and retention cysts, as well as cystic degeneration of solid tumors such as solid pseudopapillary neoplasms and pancreatic neuroendocrine neoplasms. Pancreatic juice obtained during endoscopic retrograde cholangiopancreatography has previously been used for the detection of KRAS mutation. Recently, duodenal fluid, which can be obtained during the relatively minimally invasive procedures of endoscopic ultrasound (EUS) and esophagogastroduodenoscopy, and cyst fluid collected by EUS-guided fine-needle aspiration (FNA) were used for molecular biological analysis. Furthermore, advanced analytic methods with high sensitivity were used for the detection of single and multiple markers. Early detection of malignant pancreatic tumors and risk stratification of premalignant tumors can be performed using duodenal fluid samples with a single marker with high sensitivity. Technological advances in simultaneous detection of multiple markers allow for the differentiation of cystic pancreatic tumors. One thing to note is that the clinical guidelines do not recommend pancreatic cyst fluid and pancreatic juice (PJ) sampling by EUS-FNA and endoscopic retrograde cholangiopancreatography, respectively, in actual clinical practice, but state that they be performed at experienced facilities, and duodenal fluid sampling is not mentioned in the guidelines. With improved specimen handling and the combination of markers, molecular markers in PJ samples may be used in clinical practice in the near future.
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Affiliation(s)
- Shinichi Takano
- First Department of Internal Medicine, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Mitsuharu Fukasawa
- First Department of Internal Medicine, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Nobuyuki Enomoto
- First Department of Internal Medicine, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
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7
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Rapid Multiplex Strip Test for the Detection of Circulating Tumor DNA Mutations for Liquid Biopsy Applications. BIOSENSORS 2022; 12:bios12020097. [PMID: 35200357 PMCID: PMC8869478 DOI: 10.3390/bios12020097] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/26/2022] [Accepted: 02/01/2022] [Indexed: 01/16/2023]
Abstract
In the era of personalized medicine, molecular profiling of patient tumors has become the standard practice, especially for patients with advanced disease. Activating point mutations of the KRAS proto-oncogene are clinically relevant for many types of cancer, including colorectal cancer (CRC). While several approaches have been developed for tumor genotyping, liquid biopsy has been gaining much attention in the clinical setting. Analysis of circulating tumor DNA for genetic alterations has been challenging, and many methodologies with both advantages and disadvantages have been developed. We here developed a gold nanoparticle-based rapid strip test that has been applied for the first time for the multiplex detection of KRAS mutations in circulating tumor DNA (ctDNA) of CRC patients. The method involved ctDNA isolation, PCR-amplification of the KRAS gene, multiplex primer extension (PEXT) reaction, and detection with a multiplex strip test. We have optimized the efficiency and specificity of the multiplex strip test in synthetic DNA targets, in colorectal cancer cell lines, in tissue samples, and in blood-derived ctDNA from patients with advanced colorectal cancer. The proposed strip test achieved rapid and easy multiplex detection (normal allele and three major single-point mutations) of the clinically relevant KRAS mutations in ctDNA in blood samples of CRC patients with high specificity and repeatability. This multiplex strip test represents a minimally invasive, rapid, low-cost, and promising diagnostic tool for the detection of clinically relevant mutations in cancer patients.
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Ulivi P, Passardi A, Marisi G, Chiadini E, Molinari C, Canale M, Pasini L, Ferroni F, Frassineti GL, Bartolini G, Monti M. Case Report: The Added Value of Liquid Biopsy in Advanced Colorectal Cancer From Clinical Case Experiences. Front Pharmacol 2021; 12:745701. [PMID: 34858176 PMCID: PMC8631449 DOI: 10.3389/fphar.2021.745701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Liquid biopsy represents a valid strategy for tumor molecular characterization. It gives the opportunity to bypass tumor heterogeneity, to monitor tumor characteristics during the course of treatment, and to perform the analysis even when tumor tissue is not available or inadequate. In the clinical practice of metastatic colorectal cancer, tumor molecular characterization is crucial for patient management, as RAS and BRAF status could influence the treatment choice. Although for this type of cancer tumor tissue is usually available at diagnosis, liquid biopsy could give complementary information and could permit monitoring of the mutation status during the course of treatment. At present, there are no clinical indications for its use in clinical practice. However, we report four clinical cases for which liquid biopsy analysis gave integrative information with respect to tumor tissue characterization, which permits us to understand the unresponsiveness of patients to treatment, with potential implications in patient's management.
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Affiliation(s)
- Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Alessandro Passardi
- Medical Oncology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Giorgia Marisi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Elisa Chiadini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Chiara Molinari
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Matteo Canale
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Luigi Pasini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Fabio Ferroni
- Radiology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Giovanni Luca Frassineti
- Medical Oncology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Giulia Bartolini
- Medical Oncology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Manlio Monti
- Medical Oncology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
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9
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Ye Z, Scheffer IE, Berkovic SF, Hildebrand MS. Improving Specificity of Cerebrospinal Fluid Liquid Biopsy for Genetic Testing. Ann Neurol 2021; 90:693-694. [PMID: 34374121 DOI: 10.1002/ana.26191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/09/2021] [Indexed: 02/01/2023]
Affiliation(s)
- Zimeng Ye
- Department of Medicine (Austin Health), University of Melbourne, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Department of Medicine (Austin Health), University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Samuel F Berkovic
- Department of Medicine (Austin Health), University of Melbourne, Melbourne, Victoria, Australia
| | - Michael S Hildebrand
- Department of Medicine (Austin Health), University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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10
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Okazaki S, Sasaki T, Yasuda S, Abe M, Yoshida N, Yoshida R, Ishibashi K, Minami Y, Okumura S, Chiba S, Takei H, Hayashi R, Nagato T, Kobayashi H, Sugitani A, Ono Y, Mizukami Y, Kitada M, Ohsaki Y. The feasibility of circulating tumor DNA analysis as a marker of recurrence in triple-negative breast cancer. Oncol Lett 2021; 21:420. [PMID: 33841581 DOI: 10.3892/ol.2021.12681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Triple-negative breast cancer (TNBC) has a poorer prognosis than other breast cancer subtypes; therefore, identifying markers of early recurrence is important. The present study aimed to establish a liquid biopsy protocol for droplet digital PCR-based detection of frequently mutated genes in patients with TNBC. Tumor DNA from 36 patients with TNBC who relapsed within 2 years after surgical resection was retrospectively analyzed. Somatic mutational profiles were evaluated using targeted sequencing to identify frequently mutated genes and genes associated with molecularly targeted therapies. The association between genetic alterations and associated protein phosphorylation was investigated using immunohistochemical analysis. Recurrent hot spot mutations in the plasma were monitored over time. Mutation-specific probes were used to successfully detect mutations in the blood samples of patients who were positive for PIK3CA H1047R and AKT1 E17K mutations. Somatic mutations in AKT1 (14.9%) and PIK3CA (25.5%) were frequently identified in the data. Robust phosphorylation of AKT and S6RP was more common in tumors with PIK3CA H1047R and AKT1 E17K mutational background than in tumors with wild-type PIK3CA and AKT1. In conclusion, the present study evaluated a high-sensitivity detection system for frequently mutated genes that was also applicable for cell-free DNA. The PI3K/AKT pathway was revealed to be activated in patients harboring PIK3CA H1047R and AKT1 E17K mutations; therefore, the PI3K/AKT pathway may be a promising candidate for targeted therapy in these patients.
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Affiliation(s)
- Satoshi Okazaki
- Respiratory Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Breast Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Takaaki Sasaki
- Respiratory Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Shunsuke Yasuda
- Respiratory Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Breast Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Masahiro Abe
- Respiratory Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Breast Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Nana Yoshida
- Respiratory Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Breast Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Ryohei Yoshida
- Respiratory Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Kei Ishibashi
- Respiratory Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Breast Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Yoshinori Minami
- Respiratory Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Shunsuke Okumura
- Respiratory Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Shinichi Chiba
- Center for Advanced Research and Education, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Hidehiro Takei
- Department of Surgical Pathology, Asahikawa Medical University Hospital, Asahikawa, Hokkaido 078-8510, Japan
| | - Ryusuke Hayashi
- Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Department of Pathology, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Toshihiro Nagato
- Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Department of Pathology, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Hiroya Kobayashi
- Department of Pathology, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Ayumu Sugitani
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido 065-0033, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido 065-0033, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido 065-0033, Japan.,Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Masahiro Kitada
- Respiratory Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Breast Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Yoshinobu Ohsaki
- Respiratory Center, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
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11
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Takano S, Fukasawa M, Shindo H, Takahashi E, Fukasawa Y, Kawakami S, Hayakawa H, Kuratomi N, Kadokura M, Maekawa S, Enomoto N. Digital next-generation sequencing of cell-free DNA for pancreatic cancer. JGH OPEN 2021; 5:508-516. [PMID: 33860102 PMCID: PMC8035455 DOI: 10.1002/jgh3.12530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/28/2021] [Accepted: 03/08/2021] [Indexed: 12/26/2022]
Abstract
Background and Aim The clinical applicability of digital next‐generation sequencing (dNGS), which eliminates polymerase chain reaction (PCR) and sequencing error‐derived noise by using molecular barcodes (MBs), has not been fully evaluated. We evaluated the utility of dNGS of cell‐free DNA (cfDNA) in liquid biopsies obtained from patients with pancreatic cancer. Methods Fifty‐eight patients with pancreatic cancer undergoing endoscopic ultrasound‐guided fine‐needle aspiration (EUS‐FNA) were included. Samples were subjected to sequencing of 50 cancer‐related genes using next‐generation sequencing (NGS). The results were used as reference gene alterations. NGS of cfDNA from plasma was performed for patients with a mutant allele frequency (MAF) >1% and an absolute mutant number > 10 copies/plasma mL in KRAS or GNAS by digital PCR. Sequence readings with and without MBs were compared with reference to EUS‐FNA‐derived gene alterations. Results The concordance rate between dNGS of cfDNA and EUS‐FNA‐derived gene alterations was higher with than without MBs (p = 0.039), and MAF cut‐off values in dNGS could be decreased to 0.2%. dNGS using MBs eliminated PCR and sequencing error by 74% and 68% for TP53 and all genes, respectively. Overall, dNGS detected mutations in KRAS (45%) and TP53 (26%) and copy number alterations in CCND2, CCND3, CDK4, FGFR1, and MYC, which are targets of molecular‐targeted drugs. Conclusions dNGS of cfDNA using MBs is useful for accurate detection of gene alterations even with low levels of MAFs. These results may be used to inform the development of diagnostics and therapeutics that can improve the prognosis of pancreatic cancer.
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Affiliation(s)
- Shinichi Takano
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Mitsuharu Fukasawa
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Hiroko Shindo
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Ei Takahashi
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Yoshimitsu Fukasawa
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Satoshi Kawakami
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Hiroshi Hayakawa
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Natsuhiko Kuratomi
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Makoto Kadokura
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Shinya Maekawa
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Nobuyuki Enomoto
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
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12
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Zhang W, Bream JH, Leng SX, Margolick JB. Validation of Preamplification to Improve Quantification of Cytomegalovirus DNA Using Droplet Digital Polymerase Chain Reaction. Anal Chem 2021; 93:3710-3716. [PMID: 33596050 PMCID: PMC10074994 DOI: 10.1021/acs.analchem.0c02890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Subclinical cytomegalovirus (CMV) replication is associated with strong cellular immune response and chronic inflammation, which could contribute to aging-related conditions such as cardiovascular disease and frailty. However, because of very low levels of CMV DNA present in people with chronic CMV infection, it has been difficult to explore the virologic and immunologic mechanisms of chronic low-level CMV infection and a sensitive method to monitor CMV replication is needed. Droplet digital PCR (ddPCR) has been shown to have higher precision and reproducibility than real-time quantitative PCR (qPCR) in quantifying low levels of CMV DNA, but it is not always sensitive enough for this purpose. Through rigorous validation experiments, we demonstrated that sensitivity and precision of quantification of very low levels of CMV DNA by ddPCR can be significantly increased by preamplification of samples with 10-20 cycles of conventional PCR, especially when testing CMV DNA in the presence of cellular DNA. With preamplification, we could reliably quantify down to two copies of CMV DNA, as opposed to five copies without preamplification. Further studies are needed to determine if ddPCR with preamplification can facilitate mechanistic studies of the characteristics and consequences of chronic CMV infection in aging adults.
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Affiliation(s)
- Weiying Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
| | - Jay H Bream
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States.,Graduate Program in Immunology, Johns Hopkins School of Medicine, Baltimore, Maryland 21224, United States
| | - Sean X Leng
- Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21224, United States
| | - Joseph B Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
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13
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Okada T, Mizukami Y, Ono Y, Sato H, Hayashi A, Kawabata H, Koizumi K, Masuda S, Teshima S, Takahashi K, Katanuma A, Omori Y, Iwano H, Yamada M, Yokochi T, Asahara S, Kawakubo K, Kuwatani M, Sakamoto N, Enomoto K, Goto T, Sasajima J, Fujiya M, Ueda J, Matsumoto S, Taniue K, Sugitani A, Karasaki H, Okumura T. Digital PCR-based plasma cell-free DNA mutation analysis for early-stage pancreatic tumor diagnosis and surveillance. J Gastroenterol 2020; 55:1183-1193. [PMID: 32939577 DOI: 10.1007/s00535-020-01724-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/17/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Cell-free DNA (cfDNA) shed from tumors into the circulation offers a tool for cancer detection. Here, we evaluated the feasibility of cfDNA measurement and utility of digital PCR (dPCR)-based assays, which reduce subsampling error, for diagnosing pancreatic ductal adenocarcinoma (PDA) and surveillance of intraductal papillary mucinous neoplasm (IPMN). METHODS We collected plasma from seven institutions for cfDNA measurements. Hot-spot mutations in KRAS and GNAS in the cfDNA from patients with PDA (n = 96), undergoing surveillance for IPMN (n = 112), and normal controls (n = 76) were evaluated using pre-amplification dPCR. RESULTS Upon Qubit measurement and copy number assessment of hemoglobin-subunit (HBB) and mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) in plasma cfDNA, HBB offered the best resolution between patients with PDA relative to healthy subjects [area under the curve (AUC) 0.862], whereas MT-ND1 revealed significant differences between IPMN and controls (AUC 0.851). DPCR utilizing pre-amplification cfDNA afforded accurate tumor-derived mutant KRAS detection in plasma in resectable PDA (AUC 0.861-0.876) and improved post-resection recurrence prediction [hazard ratio (HR) 3.179, 95% confidence interval (CI) 1.025-9.859] over that for the marker CA19-9 (HR 1.464; 95% CI 0.674-3.181). Capturing KRAS and GNAS could also provide genetic evidence in patients with IPMN-associated PDA and undergoing pancreatic surveillance. CONCLUSIONS Plasma cfDNA quantification by distinct measurements is useful to predict tumor burden. Through appropriate methods, dPCR-mediated mutation detection in patients with localized PDA and IPMN likely to progress to invasive carcinoma is feasible and complements conventional biomarkers.
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Affiliation(s)
- Tetsuhiro Okada
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan.
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hiroki Sato
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Akihiro Hayashi
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hidemasa Kawabata
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Kazuya Koizumi
- Center for Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
| | - Sakue Masuda
- Center for Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
| | - Shinichi Teshima
- Department of Pathology, Shonan Kamakura General Hospital, Kamakura, Japan
| | | | - Akio Katanuma
- Center for Gastroenterology, Teine-Keijinkai Hospital, Sapporo, Japan
| | - Yuko Omori
- Department of Pathology, Teine-Keijinkai Hospital, Sapporo, Japan
| | - Hirotoshi Iwano
- Department of Gastroenterology and Endoscopic Unit, Shibetsu City Hospital, Shibetsu, Japan
| | - Masataka Yamada
- Department of Gastroenterology and Endoscopic Unit, Shibetsu City Hospital, Shibetsu, Japan
| | - Tomoki Yokochi
- Department of Clinical Research, Chiba Tokushukai Hospital, Funabashi, Japan
| | - Shingo Asahara
- Department of Clinical Research, Chiba Tokushukai Hospital, Funabashi, Japan
| | - Kazumichi Kawakubo
- Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Masaki Kuwatani
- Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Naoya Sakamoto
- Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Katsuro Enomoto
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Takuma Goto
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Junpei Sasajima
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Mikihiro Fujiya
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Jun Ueda
- Center for Advanced Research and Education, Asahikawa Medical University, Asahikawa, Japan
| | - Seiji Matsumoto
- Center for Advanced Research and Education, Asahikawa Medical University, Asahikawa, Japan
| | - Kenzui Taniue
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Ayumu Sugitani
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Toshikatsu Okumura
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
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14
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Aberrant expression of a novel circular RNA in pancreatic cancer. J Hum Genet 2020; 66:181-191. [PMID: 32879441 DOI: 10.1038/s10038-020-00826-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/01/2020] [Accepted: 08/11/2020] [Indexed: 12/31/2022]
Abstract
Circular RNAs (circRNAs) are single-stranded, covalently closed RNA molecules that are produced from pre-mRNAs through a process known as back-splicing. Although circRNAs are expressed under specific conditions, current understanding of their comprehensive expression status is still limited. Here, we performed a large-scale circRNA profiling analysis in human pancreatic ductal adenocarcinoma (PDAC) tissues, using circular RNA-specific RNA sequencing. We identified more than 40,000 previously unknown circRNAs, some of which were upregulated in PDAC tissues, compared with normal pancreatic tissues. We determined the full-length sequence of a circRNA upregulated in PDAC, which was derived from two noncoding RNA loci on chromosome 12. The novel circRNA, named circPDAC RNA, was not expressed in normal human cells, but was expressed in PDAC and other carcinoma cells. While postulated biological functions, such as peptide production from the circPDAC RNA, were not detected, its aberrant expression was confirmed in other PDAC tissues and in serum from a PDAC patient. These results demonstrate that comprehensive studies are necessary to reveal the expression status of circRNAs and that the circPDAC RNA identified here might serve as a novel biomarker for cancers, including PDAC.
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15
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Ono Y, Hayashi A, Maeda C, Suzuki M, Wada R, Sato H, Kawabata H, Okada T, Goto T, Karasaki H, Mizukami Y, Okumura T. Time-saving method for directly amplifying and capturing a minimal amount of pancreatic tumor-derived mutations from fine-needle aspirates using digital PCR. Sci Rep 2020; 10:12332. [PMID: 32704002 PMCID: PMC7378187 DOI: 10.1038/s41598-020-69221-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
It is challenging to secure a cytopathologic diagnosis using minute amounts of tumor fluids and tissue fragments. Hence, we developed a rapid, accurate, low-cost method for detecting tumor cell-derived DNA from limited amounts of specimens and samples with a low tumor cellularity, to detect KRAS mutations in pancreatic ductal carcinomas (PDA) using digital PCR (dPCR). The core invention is based on the suspension of tumor samples in pure water, which causes an osmotic burst; the crude suspension could be directly subjected to emulsion PCR in the platform. We examined the feasibility of this process using needle aspirates from surgically resected pancreatic tumor specimens (n = 12). We successfully amplified and detected mutant KRAS in 11 of 12 tumor samples harboring the mutation; the positive mutation frequency was as low as 0.8%. We used residual specimens from fine-needle aspiration/biopsy and needle flush processes (n = 10) for method validation. In 9 of 10 oncogenic KRAS pancreatic tumor samples, the "water-burst" method resulted in a positive mutation call. We describe a dPCR-based, super-sensitive screening protocol for determining KRAS mutation availability using tiny needle aspirates from PDAs processed using simple steps. This method might enable pathologists to secure a more accurate, minimally invasive diagnosis using minute tissue fragments.
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Affiliation(s)
- Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Akihiro Hayashi
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Chiho Maeda
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Mayumi Suzuki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Reona Wada
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Hiroki Sato
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hidemasa Kawabata
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Tetsuhiro Okada
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Takuma Goto
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan.
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Toshikatsu Okumura
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
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16
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Ishida Y, Takano S, Maekawa S, Yamaguchi T, Yoshida T, Kobayashi S, Iwamoto F, Kuno T, Hayakawa H, Matsuda S, Fukasawa M, Shindo H, Inoue T, Nakayama Y, Ichikawa D, Sato T, Enomoto N. Fractionated small cell-free DNA increases possibility to detect cancer-related gene mutations in advanced colorectal cancer. JGH OPEN 2020; 4:978-986. [PMID: 33102773 PMCID: PMC7578331 DOI: 10.1002/jgh3.12379] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/11/2020] [Indexed: 12/19/2022]
Abstract
Background and Aim Liquid biopsy is a method that can efficiently detect tumor genetic abnormalities from body fluids such as blood and urine. Detection sensitivity and the available number of mutations in cell-free DNA (cfDNA) are limited. In this study, we develop a highly sensitive and comprehensive method to detect mutations from cfDNA by concentrating tumor fractions of small cfDNA in advanced colorectal cancers. Methods Biopsied specimens and 37 serum samples were collected from 27 patients with advanced colorectal carcinoma. A serum-extracted cfDNA was divided into enriched fractionated small cfDNA and unfractionated cfDNA. Both cfDNAs were subjected to digital polymerase chain reaction (PCR) to evaluate their KRAS, BRAF, CDKN2A, and TP53 status. Consequently, their mutant allele frequencies (MAFs) were compared and analyzed by next-generation sequencing (NGS) in conjunction with tissue-derived DNA. Results NGS analyses revealed mutations in TP53 (63%), KRAS (63%), APC (30%), and PIK3CA (22%). Digital PCR could detect mutations in 25 of 27 samples (93%) of unfractionated cfDNA, a rate that increased to 100% when samples were enriched with fractionated small cfDNA (6.8 vs 10.7%, P < 0.001). NGS also showed increased MAFs in fractionated small cfDNA compared to unfractionated cfDNA (16.3 vs 18.8%, P = 0.012) and a tendency to detect a greater number of cancer-related genes in fractionated cfDNA. Conclusions Fractionated small cfDNA increased MAFs of gene mutations and increases the possibilities to detect cancer-related genes even in advanced cancer patients from whom it is difficult to obtain tissue samples.
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Affiliation(s)
- Yasuaki Ishida
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Shinichi Takano
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Shinya Maekawa
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Tatsuya Yamaguchi
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Takashi Yoshida
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Shoji Kobayashi
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Fumihiko Iwamoto
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Toru Kuno
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Hiroshi Hayakawa
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Shuya Matsuda
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Mitsuharu Fukasawa
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Hiroko Shindo
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Taisuke Inoue
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Yasuhiro Nakayama
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Daisuke Ichikawa
- First Department of Surgery, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Tadashi Sato
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
| | - Nobuyuki Enomoto
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Yamanashi Japan
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17
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Bussaglia E, Pratcorona M, Carricondo M, Sansegundo L, Rubio MA, Monter A, Brell A, Badell I, Esteve J, Arnan M, Talarn C, Tormo M, García A, Vall-Llovera F, Ortin X, Pedro C, Bargay J, Brunet S, Sierra J, Nomdedéu J. Application of a digital PCR method for WT1 to myeloid neoplasms in CR and deep ELN WT1 molecular response (< 10 copies). Ann Hematol 2020; 99:765-772. [PMID: 32062741 DOI: 10.1007/s00277-020-03910-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/13/2020] [Indexed: 11/30/2022]
Abstract
Bone marrow WT1 mRNA levels assessed by the ELN method are useful to establish prognostic correlations in myeloid malignancies treated with chemotherapy or hematopoietic stem cell transplantation (HCT). Those patients with WT1 levels below ten copies have a good outcome. However, some of these patients relapse. To further characterize this group of cases, we applied a new and sensitive digital (ddPCR) WT1 method. A consecutive series of 49 patients with treated myeloid malignancies and with an ELN WT1 quantitation of < 10 copies were included in the study. All cases (47 AML and 2 MDS) have received intensive chemotherapy or HCT. One to four micrograms of total RNA were retrotranscribed to obtain ≥ 10,000 ABL1 copies using the ELN protocol. Only those cases with a good quality cDNA were used in the ddPCR WT1 test. The ddPCR Gene Expression WT1 Assay of Bio-Rad© was used to perform the PCR amplification, and the microdroplets were quantified in the Bio-Rad's QX200 droplet reader. Eighteen patients showed a negative WT1 ddPCR assay (0 copies/μl), whereas 31 cases were positive (results ranged from 1 to 15.2 copies/μl). Survival analysis showed statistically significant differences in terms of OS between both groups, 83 ± 8% vs. 46 ± 9% (p = 0.024). A statistically significant correlation was also found between ddPCRWT1 results and CD123+ cell number detected by flow cytometry (p = 0.024). Larger series of patients tested with the current ddPCRWT1 method will solve whether it could be used to stratify patients with myeloid malignancies achieving deep WT1 molecular response (< 10 copies).
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Affiliation(s)
- E Bussaglia
- Hematology Lab, Hematology Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Mas Casanovas, 9008041, Barcelona, Spain.,Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - M Pratcorona
- Hematology Lab, Hematology Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Mas Casanovas, 9008041, Barcelona, Spain.,Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - M Carricondo
- Hematology Lab, Hematology Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Mas Casanovas, 9008041, Barcelona, Spain.,Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - L Sansegundo
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - M A Rubio
- Hematology Lab, Hematology Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Mas Casanovas, 9008041, Barcelona, Spain.,Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - A Monter
- Hematology Lab, Hematology Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Mas Casanovas, 9008041, Barcelona, Spain.,Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - A Brell
- Hematology Lab, Hematology Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Mas Casanovas, 9008041, Barcelona, Spain.,Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - I Badell
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Pediatrics Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - J Esteve
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - M Arnan
- Hematology Department, ICO Hospitalet, L'Hospitalet de Llobregat, Spain
| | - C Talarn
- Hematology Department, Hospital Joan XXIII, Tarragona, Spain
| | - M Tormo
- Hematology Department, Hospital Clínic, Valencia, Spain
| | - A García
- Hematology Department, Hospital Arnau de Vilanova, Lleida, Spain
| | - F Vall-Llovera
- Hematology Department, Hospital de la Mutua de Terrassa, Terrassa, Spain
| | - X Ortin
- Hematology Department, Hospital Verge de La Cinta, Tortosa, Spain
| | - C Pedro
- Hematology Department, Parc de Salut Mar, Barcelona, Spain
| | - J Bargay
- Hematology Department, Hospital de Son Llatzer, Palma de Mallorca, Spain
| | - S Brunet
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - J Sierra
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - J Nomdedéu
- Hematology Lab, Hematology Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Mas Casanovas, 9008041, Barcelona, Spain. .,Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.
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18
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Kozak K, Kowalik A, Gos A, Wasag B, Lugowska I, Jurkowska M, Krawczynska N, Kosela-Paterczyk H, Switaj T, Teterycz P, Klimczak A, Siedlecki JA, Chlopek M, Kalisz J, Limon J, Rutkowski P. Cell-free DNA BRAF V600E measurements during BRAF inhibitor therapy of metastatic melanoma: long-term analysis. TUMORI JOURNAL 2020; 106:300891619900928. [PMID: 32026754 DOI: 10.1177/0300891619900928] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE We assessed the status of the BRAF V600E mutation in cell-free circulating tumor DNA (cfDNA) isolated from the plasma of patients with metastatic melanoma treated with the BRAF inhibitor vemurafenib, collected at different time points during therapy to evaluate the sensitivity and specificity of quantitative polymerase chain reaction and droplet digital polymerase chain reaction (ddPCR) and the correlation between the level of plasma cfDNA p.V600E and the long-term clinical outcome. METHODS cfDNA in patients with BRAF-mutated melanoma (n = 62) was analyzed at baseline and at 4-8 weeks from the start of vemurafenib therapy. BRAF mutations were assessed using tumor tissue-derived DNA and circulating cfDNA from plasma samples. Quantification of BRAF V600E was performed in cfDNA using ddPCR. RESULTS cfDNA V600E was detected in the plasma of 48/62 (77%) patients at baseline and in 18/62 (29%) patients after 4-8 weeks of treatment. Patients positive for BRAF mutations in cfDNA at baseline had shorter progression-free survival (PFS) and overall survival (OS) compared with patients with undetectable cfDNA BRAF mutations. Undetectable cfDNA p.V600E at baseline and after 4-8 weeks of therapy was associated with the best prognosis. When treated as a continuous variable, the log-transformed concentration of baseline cfDNA p.V600E was significantly associated with both PFS and OS. This effect was retained in the multivariate OS Cox model adjusted for Eastern Cooperative Oncology Group performance status, the presence of brain metastases, patient age, and previous systemic treatment. CONCLUSIONS Monitoring of plasma BRAF p.V600E cfDNA concentrations in patients with metastatic melanoma on targeted therapy may have prognostic value. Undetectable cfDNA p.V600E before and during treatment was associated with a favorable prognosis.
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Affiliation(s)
- Katarzyna Kozak
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Artur Kowalik
- Department of Molecular Diagnostics, Holy Cross Cancer Centre, Kielce, Poland
| | - Aleksandra Gos
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Bartosz Wasag
- Department of Molecular Biology, Medical University of Gdansk, Gdansk, Poland
| | - Iwona Lugowska
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | | | - Natalia Krawczynska
- Department of Molecular Biology, Medical University of Gdansk, Gdansk, Poland
| | - Hanna Kosela-Paterczyk
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Tomasz Switaj
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Paweł Teterycz
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Anna Klimczak
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Małgorzata Chlopek
- Department of Molecular Diagnostics, Holy Cross Cancer Centre, Kielce, Poland
| | - Joanna Kalisz
- Department of Molecular Diagnostics, Holy Cross Cancer Centre, Kielce, Poland
| | - Janusz Limon
- Department of Molecular Biology, Medical University of Gdansk, Gdansk, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
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19
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Bach S, Sluiter NR, Beagan JJ, Mekke JM, Ket JCF, van Grieken NCT, Steenbergen RDM, Ylstra B, Kazemier G, Tuynman JB. Circulating Tumor DNA Analysis: Clinical Implications for Colorectal Cancer Patients. A Systematic Review. JNCI Cancer Spectr 2019; 3:pkz042. [PMID: 32328554 PMCID: PMC7050033 DOI: 10.1093/jncics/pkz042] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/21/2019] [Accepted: 06/05/2019] [Indexed: 02/06/2023] Open
Abstract
Background Liquid biopsies could improve diagnosis, prognostication, and monitoring of colorectal cancer (CRC). Mutation, chromosomal copy number alteration, and methylation analysis in circulating tumor DNA (ctDNA) from plasma or serum has gained great interest. However, the literature is inconsistent on preferred candidate markers, hampering a clear direction for further studies and clinical translation. This review assessed the potential of ctDNA analysis for clinical utility. Methods A systematic review according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines was conducted up to December 3, 2018, followed by methodological quality assessment. Primary endpoints were accuracy for detection, prognostication, and monitoring. Results Eighty-four studies were included. For CRC detection, sensitivity was 75% using ctDNA mutation analysis and up to 96% using copy number analysis. Septin 9 (SEPT9) hypermethylation analysis showed sensitivities of 100% and specificities of 97%. Regarding prognostication, ctDNA KRAS mutations were associated with oncological outcome and could predict response to anti-epidermal growth factor receptor therapy. For monitoring, sequential ctDNA KRAS mutation analysis showed promise for detection of relapses or therapy resistance. Conclusions This comprehensive overview of ctDNA candidate markers demonstrates SEPT9 methylation analysis to be promising for CRC detection, and KRAS mutation analysis could assist in prognostication and monitoring. Prospective evaluation of marker panels in clinical decision making should bring ctDNA analysis into practice.
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Affiliation(s)
- Sander Bach
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Nina R Sluiter
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Jamie J Beagan
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Joost M Mekke
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Johannes C F Ket
- Medical Information Specialist/Literature Researcher Medical Library, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Nicole C T van Grieken
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Geert Kazemier
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Jurriaan B Tuynman
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
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20
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Chen-Yin O, Vu T, Grunwald JT, Toledano M, Zimak J, Toosky M, Shen B, Zell JA, Gratton E, Abram T, Zhao W. An ultrasensitive test for profiling circulating tumor DNA using integrated comprehensive droplet digital detection. LAB ON A CHIP 2019; 19:993-1005. [PMID: 30735225 PMCID: PMC6559803 DOI: 10.1039/c8lc01399c] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Current cancer detection systems lack the required sensitivity to reliably detect minimal residual disease (MRD) and recurrence at the earliest stages when treatment would be most effective. To address this issue, we present a novel liquid biopsy approach that utilizes an integrated comprehensive droplet digital detection (IC3D) digital PCR system which combines microfluidic droplet partitioning, fluorescent multiplex PCR chemistry, and our rapid 3D, large-volume droplet counting technology. The IC3D ddPCR assay can detect cancer-specific, ultra-rare genomic targets due to large sample input and high degree of partitioning. We first demonstrate our droplet digital PCR assay can robustly detect common cancer mutants including KRAS G12D spiked in wild-type genomic background or isolated from patient samples with 100% specificity. We then demonstrate that the IC3D ddPCR system can detect oncogenic KRAS G12D mutant alleles against a background of wild-type genomes at a sensitivity of 0.00125-0.005% with a false positive rate of 0% which is 50 to 1000× more sensitive than existing commercial liquid biopsy ddPCR and qPCR platforms, respectively. In addition, our technology can uniquely enable detection of circulating tumor cells using their genetic markers without a pre-enrichment step, and analysis of total tumor DNA isolated from blood samples, which will increase clinical sensitivity and specificity, and minimize inter-assay variability. Therefore, our technology holds the potential to provide clinicians with a powerful decision-making tool to monitor and treat MRD with unprecedented sensitivity for earlier stage intervention.
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Affiliation(s)
- Ou Chen-Yin
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Tam Vu
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Michael Toledano
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Jan Zimak
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Melody Toosky
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Byron Shen
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Jason A. Zell
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
- Division of Hematology/Oncology, University of California Irvine Medical Center, Orange, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA
| | - Tim Abram
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Division of Hematology/Oncology, University of California Irvine Medical Center, Orange, USA
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21
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Omori Y, Ono Y, Tanino M, Karasaki H, Yamaguchi H, Furukawa T, Enomoto K, Ueda J, Sumi A, Katayama J, Muraki M, Taniue K, Takahashi K, Ambo Y, Shinohara T, Nishihara H, Sasajima J, Maguchi H, Mizukami Y, Okumura T, Tanaka S. Pathways of Progression From Intraductal Papillary Mucinous Neoplasm to Pancreatic Ductal Adenocarcinoma Based on Molecular Features. Gastroenterology 2019; 156:647-661.e2. [PMID: 30342036 DOI: 10.1053/j.gastro.2018.10.029] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 09/14/2018] [Accepted: 10/05/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Intraductal papillary mucinous neoplasms (IPMNs) are regarded as precursors of pancreatic ductal adenocarcinomas (PDAs), but little is known about the mechanism of progression. This makes it challenging to assess cancer risk in patients with IPMNs. We investigated associations of IPMNs with concurrent PDAs by genetic and histologic analyses. METHODS We obtained 30 pancreatic tissues with concurrent PDAs and IPMNs, and 168 lesions, including incipient foci, were mapped, microdissected, and analyzed for mutations in 18 pancreatic cancer-associated genes and expression of tumor suppressors. RESULTS We determined the clonal relatedness of lesions, based on driver mutations shared by PDAs and concurrent IPMNs, and classified the lesions into 3 subtypes. Twelve PDAs contained driver mutations shared by all concurrent IPMNs, which we called the sequential subtype. This subset was characterized by less diversity in incipient foci with frequent GNAS mutations. Eleven PDAs contained some driver mutations that were shared with concurrent IPMNs, which we called the branch-off subtype. In this subtype, PDAs and IPMNs had identical KRAS mutations but different GNAS mutations, although the lesions were adjacent. Whole-exome sequencing and methylation analysis of these lesions indicated clonal origin with later divergence. Ten PDAs had driver mutations not found in concurrent IPMNs, called the de novo subtype. Expression profiles of TP53 and SMAD4 increased our ability to differentiate these subtypes compared with sequencing data alone. The branch-off and de novo subtypes had substantial heterogeneity among early clones, such as differences in KRAS mutations. Patients with PDAs of the branch-off subtype had a longer times of disease-free survival than patients with PDAs of the de novo or the sequential subtypes. CONCLUSIONS Detailed histologic and genetic analysis of PDAs and concurrent IPMNs identified 3 different pathways by which IPMNs progress to PDAs-we call these the sequential, branch-off, and de novo subtypes. Subtypes might be associated with clinical and pathologic features and be used to select surveillance programs for patients with IPMNs.
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Affiliation(s)
- Yuko Omori
- Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan; Department of Pathology, Teine-Keijinkai Hospital, Sapporo, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Mishie Tanino
- Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Hiroshi Yamaguchi
- Division of Diagnostic Pathology, Tokyo Medical University, Tokyo, Japan
| | - Toru Furukawa
- Department of Histopathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Katsuro Enomoto
- Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Jun Ueda
- Center for Advanced Research and Education, Asahikawa Medical University, Asahikawa, Japan
| | - Atsuko Sumi
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Jin Katayama
- Diagnostic Partnering, Clinical Sequencing Division, Thermo Fisher Scientific, Tokyo, Japan
| | | | - Kenzui Taniue
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan; Genomedia Inc., Tokyo, Japan
| | | | - Yoshiyasu Ambo
- Department of Surgery, Teine-Keijinkai Hospital, Sapporo, Japan
| | | | | | - Junpei Sasajima
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Hiroyuki Maguchi
- Center for Gastroenterology, Teine-Keijinkai Hospital, Sapporo, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, Japan.
| | | | - Shinya Tanaka
- Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
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22
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Okada T, Iwano H, Ono Y, Karasaki H, Sato T, Yamada M, Omori Y, Sato H, Hayashi A, Kawabata H, Goto T, Sasajima J, Takauji S, Nagashima K, Mizukami Y, Okumura T. Utility of "liquid biopsy" using pancreatic juice for early detection of pancreatic cancer. Endosc Int Open 2018; 6:E1454-E1461. [PMID: 30539069 PMCID: PMC6288761 DOI: 10.1055/a-0721-1747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/03/2018] [Indexed: 02/08/2023] Open
Abstract
Background Despite advances in the diagnosis of pancreatic ductal adenocarcinoma (PDA), histological evaluation of small and poorly defined masses in the pancreas is uncomfortable and unsafe. Methods We herein report a case of early stage PDA, in which multiple KRAS mutations were detected in the pancreatic juice preoperatively. A small hypoechoic area adjacent to the portal vein was detected through endoscopic ultrasound in the pancreatic body. KRAS mutations were evaluated using plasma, and the pancreatic juice by digital PCR. Results Pancreatic duct biopsy and pancreatic juice cytology were performed with no evidence of malignancy; however, KRAS mutations, KRAS G12V and G12D, were detected in the pancreatic juice. Histological assessment of the resected specimen demonstrated a solid tumor with desmoplastic reaction accompanied by carcinoma in situ in the main pancreatic duct where KRAS G12V mutation was identified. More detailed analysis demonstrated KRAS G12D mutation in the cluster of low grade pancreatic intraepithelial neoplasia, implying that the lesion developed independently. Conclusions Our study indicates the potential of "endoscopic liquid biopsy" to capture the driver gene for PDA diagnosis.
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Affiliation(s)
- Tetsuhiro Okada
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido 065-0033, Japan
- Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Hirotoshi Iwano
- Department of Gastroenterology and Endoscopic Unit, Shibetsu City Hospital, Shibetsu, Hokkaido 095-0048, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido 065-0033, Japan
- Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido 065-0033, Japan
- Department of Surgery, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido 065-0033, Japan
| | - Takayuki Sato
- Department of Gastroenterology and Endoscopic Unit, Shibetsu City Hospital, Shibetsu, Hokkaido 095-0048, Japan
| | - Masataka Yamada
- Department of Gastroenterology and Endoscopic Unit, Shibetsu City Hospital, Shibetsu, Hokkaido 095-0048, Japan
| | - Yuko Omori
- Department of Histopathology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Hiroki Sato
- Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Akihiro Hayashi
- Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Hidemasa Kawabata
- Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Takuma Goto
- Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Junpei Sasajima
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido 065-0033, Japan
- Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Shuhei Takauji
- Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Kazuo Nagashima
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido 065-0033, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido 065-0033, Japan
- Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
- Corresponding author Yusuke Mizukami, MD PhD Institute of Biomedical ResearchSapporo Higashi Tokushukai Hospital3-1, North-33East-14 Higashi-KuSapporoHokkaido 065-0033Japan+81-11-7883628
| | - Toshikatsu Okumura
- Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
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23
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Preamplification with dUTP and Cod UNG Enables Elimination of Contaminating Amplicons. Int J Mol Sci 2018; 19:ijms19103185. [PMID: 30332749 PMCID: PMC6214100 DOI: 10.3390/ijms19103185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/04/2018] [Accepted: 10/14/2018] [Indexed: 11/17/2022] Open
Abstract
Analyzing rare DNA and RNA molecules in limited sample sizes, such as liquid biopsies and single cells, often requires preamplification, which makes downstream analyses particularly sensitive to polymerase chain reaction (PCR) generated contamination. Herein, we assessed the feasibility of performing Cod uracil-DNA N-glycosylase (Cod UNG) treatment in combination with targeted preamplification, using deoxyuridine triphosphate (dUTP) to eliminate carry-over DNA. Cod UNG can be completely and irreversibly heat inactivated, a prerequisite in preamplification methods, where any loss of amplicons is detrimental to subsequent quantification. Using 96 target assays and quantitative real-time PCR, we show that replacement of deoxythymidine triphosphate (dTTP) with dUTP in the preamplification reaction mix results in comparable dynamic range, reproducibility, and sensitivity. Moreover, Cod UNG essentially removes all uracil-containing template of most assays, regardless of initial concentration, without affecting downstream analyses. Finally, we demonstrate that the use of Cod UNG and dUTP in targeted preamplification can easily be included in the workflow for single-cell gene expression profiling. In summary, Cod UNG treatment in combination with targeted preamplification using dUTP provides a simple and efficient solution to eliminate carry-over contamination and the generation of false positives and inaccurate quantification.
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