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Cleveland MH, He HJ, Milavec M, Bae YK, Vallone PM, Huggett JF. Digital PCR for the characterization of reference materials. Mol Aspects Med 2024; 96:101256. [PMID: 38359699 DOI: 10.1016/j.mam.2024.101256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
Well-characterized reference materials support harmonization and accuracy when conducting nucleic acid-based tests (such as qPCR); digital PCR (dPCR) can measure the absolute concentration of a specific nucleic acid sequence in a background of non-target sequences, making it ideal for the characterization of nucleic acid-based reference materials. National Metrology Institutes are increasingly using dPCR to characterize and certify their reference materials, as it offers several advantages over indirect methods, such as UV-spectroscopy. While dPCR is gaining widespread adoption, it requires optimization and has certain limitations and considerations that users should be aware of when characterizing reference materials. This review highlights the technical considerations of dPCR, as well as its role when developing and characterizing nucleic acid-based reference materials.
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Affiliation(s)
- Megan H Cleveland
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA.
| | - Hua-Jun He
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Young-Kyung Bae
- Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
| | - Peter M Vallone
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Jim F Huggett
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
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2
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Meng P, Dalal H, Chen Y, Brueffer C, Gladchuk S, Alcaide M, Ehinger A, Saal LH. Digital PCR quantification of ultrahigh ERBB2 copy number identifies poor breast cancer survival after trastuzumab. NPJ Breast Cancer 2024; 10:14. [PMID: 38374091 PMCID: PMC10876644 DOI: 10.1038/s41523-024-00621-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
HER2/ERBB2 evaluation is necessary for treatment decision-making in breast cancer (BC), however current methods have limitations and considerable variability exists. DNA copy number (CN) evaluation by droplet digital PCR (ddPCR) has complementary advantages for HER2/ERBB2 diagnostics. In this study, we developed a single-reaction multiplex ddPCR assay for determination of ERBB2 CN in reference to two control regions, CEP17 and a copy-number-stable region of chr. 2p13.1, validated CN estimations to clinical in situ hybridization (ISH) HER2 status, and investigated the association of ERBB2 CN with clinical outcomes. 909 primary BC tissues were evaluated and the area under the curve for concordance to HER2 status was 0.93 and 0.96 for ERBB2 CN using either CEP17 or 2p13.1 as reference, respectively. The accuracy of ddPCR ERBB2 CN was 93.7% and 94.1% in the training and validation groups, respectively. Positive and negative predictive value for the classic HER2 amplification and non-amplification groups was 97.2% and 94.8%, respectively. An identified biological "ultrahigh" ERBB2 ddPCR CN group had significantly worse survival within patients treated with adjuvant trastuzumab for both recurrence-free survival (hazard ratio, HR: 3.3; 95% CI 1.1-9.6; p = 0.031, multivariable Cox regression) and overall survival (HR: 3.6; 95% CI 1.1-12.6; p = 0.041). For validation using RNA-seq data as a surrogate, in a population-based SCAN-B cohort (NCT02306096) of 682 consecutive patients receiving adjuvant trastuzumab, the ultrahigh-ERBB2 mRNA group had significantly worse survival. Multiplex ddPCR is useful for ERBB2 CN estimation and ultrahigh ERBB2 may be a predictive factor for decreased long-term survival after trastuzumab treatment.
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Affiliation(s)
- Pei Meng
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
| | - Hina Dalal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
| | - Yilun Chen
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Christian Brueffer
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Sergii Gladchuk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Miguel Alcaide
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden.
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Zhang X, Wang S, Wang J, Sun X, Xue J, Wang Z, Yang T, Weng L, Wang B, Luo G. A ddPCR platform based on a microfluidic chip with a dual-function flow-focusing structure for sample-to-result DNA quantification analysis. LAB ON A CHIP 2024; 24:738-750. [PMID: 38192250 DOI: 10.1039/d3lc01078c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Droplet digital PCR (ddPCR) is a powerful method for absolute nucleic acid quantification with high precision and accuracy. However, complicated operational steps have hampered the use and diffusion of ddPCR. Therefore, an automated, easy-to-use, low-sample-consumption, and portable ddPCR platform is urgently needed. This paper proposes a microfluidic ddPCR platform based on a microfluidic chip that can realize the sample-to-result function by switching the rotary valve, achieving the dual function of the flow-focusing structure for droplet generation and readout. Sample, generation oil, and analysis oil were pre-added to the reservoirs. Droplets were generated due to focusing flow, and after passing through the integrated temporary storage bin in the rotary valve, the droplets and oil subsequently entered the collecting tube, improving the droplet-to-oil volume ratio for enhanced thermal cycle performance. Droplets with an average diameter of 107.44 μm and a CV of 2.38% were generated using our chip under the optimal pressures. High-performance thermal cycling was achieved through improvements of the droplet-to-oil volume ratio of the sample, the integrated heating lid, the pure copper heating base, and the temperature-controlling algorithm. Gradient quantification experiments were conducted for the HER2 and CEP17 genes extracted from breast cancer cells, yielding strong linear correlations with R2 values of 0.9996 for FAM and 0.9989 for CY5. Moreover, pronounced linearity was obtained between the detected concentrations of HER2 and CEP17, indicated by a slope of 1.0091 and an R2 of 0.9997, signifying consistent HER2 : CEP17 ratios across various sample dilutions. The outcomes of the quantitative analysis, encompassing the dynamic range and the consistency of the HER2 : CEP17 ratio using our ddPCR platform, meet the standards required for breast cancer assessment and therapy. Our ddPCR platform is automated, portable, and capable of stable droplet generation, high-efficiency amplification, realization of the sample-to-result function based on dual-function flow-focusing structure, and accuracy absolute quantification, underscoring its significant potential for ddPCR analysis in clinical diagnostics.
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Affiliation(s)
- Xiaoliang Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Shun Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Jinxian Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Xiaojie Sun
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Jinbing Xue
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Zhenya Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Tianhang Yang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Liangfei Weng
- Suzhou Guoke Medical Science & Technology Development Co. Ltd, Suzhou 215163, People's Republic of China
| | - Bidou Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Gangyin Luo
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
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4
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Ma Y, Gan J, Bai Y, Cao D, Jiao Y. Minimal residual disease in solid tumors: an overview. Front Med 2023; 17:649-674. [PMID: 37707677 DOI: 10.1007/s11684-023-1018-6] [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: 02/22/2023] [Accepted: 06/24/2023] [Indexed: 09/15/2023]
Abstract
Minimal residual disease (MRD) is termed as the small numbers of remnant tumor cells in a subset of patients with tumors. Liquid biopsy is increasingly used for the detection of MRD, illustrating the potential of MRD detection to provide more accurate management for cancer patients. As new techniques and algorithms have enhanced the performance of MRD detection, the approach is becoming more widely and routinely used to predict the prognosis and monitor the relapse of cancer patients. In fact, MRD detection has been shown to achieve better performance than imaging methods. On this basis, rigorous investigation of MRD detection as an integral method for guiding clinical treatment has made important advances. This review summarizes the development of MRD biomarkers, techniques, and strategies for the detection of cancer, and emphasizes the application of MRD detection in solid tumors, particularly for the guidance of clinical treatment.
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Affiliation(s)
- Yarui Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jingbo Gan
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Yinlei Bai
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Dandan Cao
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Yuchen Jiao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Kang YK, Si YR, Ju J, Jia ZQ, Hu NL, Dong H, Wang X, Yue J, Jiang PD, Li ZL, Zhang YY, Wang Y, Xu BH, Yuan P. Assessing early changes in plasma HER2 levels is useful for predicting therapeutic response in advanced breast cancer: A multicenter, prospective, noninterventional clinical study. Cancer Med 2023; 12:5323-5333. [PMID: 36281495 PMCID: PMC10028130 DOI: 10.1002/cam4.5352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 08/18/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Early prediction of treatment response is crucial for the optimal treatment of advanced breast cancer. We aimed to explore whether monitoring early changes in plasma human epidermal growth factor receptor 2 (HER2) levels using digital PCR (dPCR) could predict the treatment response in advanced breast cancer. METHODS This was a multicenter, prospective, noninterventional clinical study of patients with advanced breast cancer. All enrolled patients underwent blood testing to measure the HER2 levels by digital PCR before treatment initiation and once every 3 weeks during the study. The primary endpoints werea the diagnostic value of dPCR for detecting HER2 status in the blood andb the relevance of potential changes in the plasma HER2 level at 3 weeks from baseline for predicting treatment response. RESULTS Overall, 85 patients were enrolled between October 9, 2018, and January 23, 2020. dPCR had a specificity of 91.67% (95% CI: 80.61% to 97.43%) for detecting HER2 amplification, and the area under the receiver operating characteristic (ROC) curve was 0.84 (p < 0.01). A clinically relevant specificity threshold of approximately 90%, which was equivalent to a ≥15% decrease in the plasma HER2 ratio at 3 weeks from baseline, showed a positive predictive value of 97.37% (95% CI: 77.11% to 98.65%) in terms of predicting clinical benefit. Patients whose plasma HER2 ratio was reduced by ≥15% had a longer median progression-free survival (PFS) than those whose ratio was reduced by <15% (9.20 months vs. 4.50 months, p < 0.01). CONCLUSIONS Early changes in the plasma HER2 ratio may predict the treatment response in patients with advanced breast cancer and could facilitate optimal treatment selection.
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Affiliation(s)
- Yi-Kun Kang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yi-Ran Si
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jie Ju
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | | | - Nan-Lin Hu
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | | | - Xue Wang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Pei-Di Jiang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | | | | | - Yan Wang
- Gnomegen, San Diego, California, USA
| | - Bing-He Xu
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
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Establishment and evaluation of digital PCR methods for HER2 copy number variation in breast cancer. Anal Bioanal Chem 2023; 415:725-733. [PMID: 36571590 DOI: 10.1007/s00216-022-04466-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 12/27/2022]
Abstract
Accurate measurement of human epidermal growth factor receptor 2 (HER2) copy number variation (CNV) is very important for guiding the tumor target therapy in breast cancer. Digital PCR (dPCR) is a sensitive and an absolute quantitative method, which can be used to detect HER2 CNV. Three HER2 exon-specific digital PCR assays along with three new reference genes assays (homo sapiens ribonuclease P RNA component H1 (RPPH1), glucose-6-phosphate isomerase (GPI), and chromosome 1 open reading frame 43 (C1ORF43), on different chromosomes) were established and validated by using standard reference material, 8 different cell lines and 110 clinical Formalin-fixed and paraffin-embedded (FFPE) samples. DPCR can achieve precise quantification of HER2 CNV by calculating the ratio of HER2/reference gene. The positive and negative coincidence rates were 98% (53/54) and 95% (53/56), respectively, compared with fluorescence in situ hybridization (FISH) diagnostic result 110 of FFPE samples. The common reference gene CEP17 used for FISH diagnostic was not suitable as single reference gene for HER2 CNV measurements by dPCR. The best practice of HER2 CNV determination by dPCR is to conduct the three duplex assays of H1 (HER2 exon 4) with the proposed three new reference genes, with a positive cut-off value of H1/RPPH1 ≥ 2.0 or H1/averaged reference gene ≥ 2.0. The proposed dPCR method in our study can accurately provide absolute copy number of HER2 and reference gene on an alternative chromosome, thus avoiding false negative caused by polysomy of chromosome 17. The improved molecular typing and diagnosis of breast cancer will better guide clinical medication.
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7
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O'Hern K, Barney R, Chambers M, Baker C, Stevanovic M, Tsongalis GJ, Hughes E, Sriharan A. A novel method to assess copy number variation in melanoma: Droplet digital PCR for precise quantitation of the RREB1 gene in formalin-fixed, paraffin-embedded melanocytic neoplasms, a proof-of-concept study. J Cutan Pathol 2023; 50:169-177. [PMID: 36325821 DOI: 10.1111/cup.14352] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Melanocytic neoplasms can be challenging to diagnose. One well-established diagnostic aid is the detection of copy number variation (CNV) in a few key genetic loci using conventional methods such as fluorescence in situ hybridization (FISH) and chromosomal microarray (CMA). Droplet digital polymerase chain reaction (ddPCR) is a novel, cost-effective, rapid, and automated method to detect CNV. METHODS We perform the first investigation of ddPCR to assay Ras-responsive element-binding protein-1 (RREB1), the most common CNV in melanoma using formalin-fixed, paraffin-embedded (FFPE) melanocytic lesion samples; CMA data are used as the gold standard. Archival samples from 2013 to 2021 were analyzed, including 153 data points from 39 FFPE samples representing 34 patients. Benign, borderline, malignant, and metastatic melanocytic neoplasms were examined. RESULTS ddPCR showed a sensitivity and specificity of 93.8% and 95.7% using one reference gene, and 87.5% and 100% using a different reference gene for RREB1 gain detection. CONCLUSIONS Here we show that ddPCR can provide inexpensive, rapid, and robust data on the commonest copy number alteration in melanoma. Future development and validation could provide a useful ancillary tool in the diagnosis of challenging melanocytic lesions.
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Affiliation(s)
- Keegan O'Hern
- Dartmouth Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Rachael Barney
- Clinical Genomics and Advanced Technology Laboratory, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Meagan Chambers
- Dartmouth Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Catherine Baker
- Dartmouth Geisel School of Medicine, Hanover, New Hampshire, USA
| | | | - Gregory J Tsongalis
- Clinical Genomics and Advanced Technology Laboratory, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Edward Hughes
- Clinical Genomics and Advanced Technology Laboratory, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Aravindhan Sriharan
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
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Wu Y, Zhong R, Ma F. HER2-low breast cancer: Novel detections and treatment advances. Crit Rev Oncol Hematol 2023; 181:103883. [PMID: 36427769 DOI: 10.1016/j.critrevonc.2022.103883] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/20/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Breast cancer (BC), which has the highest cancer incidence in women, seriously threatens women's health. Since human epidermal growth factor receptor-2 (HER2) characterization, breast cancer treatment has entered an era of individualized targeted therapy. With the emergence of anti-HER2 targeting agents, monoclonal antibodies (mAbs) and tyrosine kinase inhibitors have considerably improved the prognosis of HER2-positive BC. However, HER2-low BC, accounting for 45-55% of BC patients, is less likely to benefit from conventional HER2-targeting mAbs. The growing success of the new generation of drugs, especially promising HER2-directed antibody-drug conjugates, has changed the treatment landscape for patients with HER2-low BC, leading to a research boom. HER-2-low BC is a heterogeneous entity, and there many areas remain to be explored. In this article, we review the literature on HER2-low BC, mainly focusing on its detection assays, clinicopathological profiles and treatment landscape, and hopefully provide insight into future perspectives.
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Affiliation(s)
- Yun Wu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruiqi Zhong
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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9
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Apolónio JD, Dias JS, Fernandes MT, Komosa M, Lipman T, Zhang CH, Leão R, Lee D, Nunes NM, Maia AT, Morera JL, Vicioso L, Tabori U, Castelo-Branco P. THOR is a targetable epigenetic biomarker with clinical implications in breast cancer. Clin Epigenetics 2022; 14:178. [PMID: 36529814 PMCID: PMC9759897 DOI: 10.1186/s13148-022-01396-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Breast cancer (BC) is the most frequently diagnosed cancer and a leading cause of death among women worldwide. Early BC is potentially curable, but the mortality rates still observed among BC patients demonstrate the urgent need of novel and more effective diagnostic and therapeutic options. Limitless self-renewal is a hallmark of cancer, governed by telomere maintenance. In around 95% of BC cases, this process is achieved by telomerase reactivation through upregulation of the human telomerase reverse transcriptase (hTERT). The hypermethylation of a specific region within the hTERT promoter, termed TERT hypermethylated oncological region (THOR) has been associated with increased hTERT expression in cancer. However, its biological role and clinical potential in BC have never been studied to the best of our knowledge. Therefore, we aimed to investigate the role of THOR as a biomarker and explore the functional impact of THOR methylation status in hTERT upregulation in BC. RESULTS THOR methylation status in BC was assessed by pyrosequencing on discovery and validation cohorts. We found that THOR is significantly hypermethylated in malignant breast tissue when compared to benign tissue (40.23% vs. 12.81%, P < 0.0001), differentiating malignant tumor from normal tissue from the earliest stage of disease. Using a reporter assay, the addition of unmethylated THOR significantly reduced luciferase activity by an average 1.8-fold when compared to the hTERT core promoter alone (P < 0.01). To further investigate its biological impact on hTERT transcription, targeted THOR demethylation was performed using novel technology based on CRISPR-dCas9 system and significant THOR demethylation was achieved. Cells previously demethylated on THOR region did not develop a histologic cancer phenotype in in vivo assays. Additional studies are required to validate these observations and to unravel the causality between THOR hypermethylation and hTERT upregulation in BC. CONCLUSIONS THOR hypermethylation is an important epigenetic mark in breast tumorigenesis, representing a promising biomarker and therapeutic target in BC. We revealed that THOR acts as a repressive regulatory element of hTERT and that its hypermethylation is a relevant mechanism for hTERT upregulation in BC.
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Affiliation(s)
- Joana Dias Apolónio
- grid.7157.40000 0000 9693 350XFaculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center Research Institute (ABC-RI), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center (ABC), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - João S. Dias
- University Hospital Center of Algarve, Faro, Portugal
| | - Mónica Teotónio Fernandes
- grid.7157.40000 0000 9693 350XAlgarve Biomedical Center Research Institute (ABC-RI), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center (ABC), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XEscola Superior de Saúde (ESSUAlg), Universidade Do Algarve, Faro, Portugal
| | - Martin Komosa
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Tatiana Lipman
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Cindy H. Zhang
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Ricardo Leão
- grid.8051.c0000 0000 9511 4342Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Donghyun Lee
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Nuno Miguel Nunes
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Ana-Teresa Maia
- grid.7157.40000 0000 9693 350XFaculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center (ABC), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XCenter for Research in Health Technologies and Information Systems (CINTESIS@RISE), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal
| | | | - Luis Vicioso
- grid.10215.370000 0001 2298 7828Faculty of Medicine, Department of Histology and Pathological Anatomy, University of Malaga, Malaga, Spain
| | - Uri Tabori
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON Canada
| | - Pedro Castelo-Branco
- grid.7157.40000 0000 9693 350XFaculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center Research Institute (ABC-RI), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center (ABC), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.421010.60000 0004 0453 9636Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
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10
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Tsuriel S, Hannes V, Hasona A, Raz M, Hershkovitz D. Digital PCR-Based Method for Detecting CDKN2A Loss in Brain Tumours. Mol Diagn Ther 2022; 26:689-698. [PMID: 36129665 DOI: 10.1007/s40291-022-00610-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 12/30/2022]
Abstract
INTRODUCTION CDKN2A is a key tumour suppressor gene and loss of CDKN2A can be found in many tumours. In astrocytoma grade IV, CDKN2A is deleted in more than 50% of tumours. In many instances, low-grade gliomas with homozygous loss of CDKN2A behave like high grade tumours. The available techniques for CDKN2A loss are laborious, expensive, unreliable, or unavailable in most pathology institutes. Therefore, although it is essential for accurate brain tumour diagnosis, the routine diagnosis does not include testing for CDKN2A deletion. METHODS We developed a digital polymerase chain reaction (dPCR) assay for CDKN2A loss detection. The assay is based on counting the copy number of CDKN2A gene and of a reference gene on the same chromosome. It was tested for the detection limit with regard to tumour content and minimal DNA quantity. It was then tested on 24 clinical samples with known CDKN2A status. Additionally, we tested 44 gliomas with unknown CDKN2A status. RESULTS We found that the newly developed assay is reliable in tissue with more than 50% tumour content and more than 0.4 ng of DNA. The validation cohort showed complete concordance, and we were able to detect homozygous loss in 16 gliomas with unknown CDKN2A status. DISCUSSION The method presented can give a fast, cost-effective, clinically reliable evaluation of CDKN2A loss in tissue with more than 50% tumour content. Its ability to work with old samples and with low amounts of DNA makes it the favoured assay in cases where other techniques fail.
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Affiliation(s)
- Shlomo Tsuriel
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel.
| | - Victoria Hannes
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
| | - Asala Hasona
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | - Michal Raz
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
| | - Dov Hershkovitz
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel.
- Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel.
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11
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Wei Y, An X, Cao Q, Che N, Xue Y, Deng H, Wang Q, Zhou R. Lentiviral vector–based xenograft tumors as candidate reference materials for detection of HER2-low breast cancer. Front Oncol 2022; 12:955943. [PMID: 36052254 PMCID: PMC9425432 DOI: 10.3389/fonc.2022.955943] [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: 05/29/2022] [Accepted: 07/14/2022] [Indexed: 12/09/2022] Open
Abstract
The human epidermal growth factor receptor 2 (HER2) is an important biomarker that plays a pivotal role in therapeutic decision-making for patients with breast cancer (BC). Patients with HER2-low BC can benefit from new HER2 targeted therapy. For ensuring the accurate and reproducible detection of HER2-low cancer, reliable reference materials are required for monitoring the sensitivity and specificity of detection assays. Herein, a lentiviral vector was used to transduce the HER2 gene into MDA-MB-231 cells that exhibited low HER2 density, and the cells were characterized by droplet digital PCR to accurately determine the copy number variation. Then, the formalin-fixed paraffin-embedded (FFPE) samples from xenografts were prepared and evaluated for suitability as candidate reference materials by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). The FFPE reference materials were selected on the basis of IHC score of 2+ and negative FISH result to meet the requirement for HER2-low BC detection. Furthermore, the FFPE reference materials exhibited typical histological structures that resembled the clinical BC specimens. These novel FFPE reference materials displayed the high stability and homogeneity, and they were produced in high quantity. In summary, we generated high-quality reference materials for internal quality control and proficiency testing in HER2-low detection.
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Affiliation(s)
- Yali Wei
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, The Third Clinical Medical College of Capital Medical University, Beijing, China
| | - Xu An
- Department of Clinical Laboratory, Tongzhou Maternal and Child Health Hospital of Beijing, Beijing, China
| | - Qinmei Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Clinical Medical College of Capital Medical University, Beijing, China
| | - Nanying Che
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Xue
- Ministry of Education (MOE) Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haiteng Deng
- Ministry of Education (MOE) Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qingtao Wang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, The Third Clinical Medical College of Capital Medical University, Beijing, China
- *Correspondence: Qingtao Wang, ; Rui Zhou,
| | - Rui Zhou
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, The Third Clinical Medical College of Capital Medical University, Beijing, China
- *Correspondence: Qingtao Wang, ; Rui Zhou,
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12
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Kim G, Lee SK, Suh DH, Kim K, No JH, Kim YB, Kim H. Clinical evaluation of a droplet digital PCR assay for detecting POLE mutations and molecular classification of endometrial cancer. J Gynecol Oncol 2021; 33:e15. [PMID: 34910396 PMCID: PMC8899877 DOI: 10.3802/jgo.2022.33.e15] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/21/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022] Open
Abstract
Objective We evaluated droplet digital polymerase chain reaction (ddPCR) method for detecting POLE mutations in endometrial cancer (EC) and guiding its molecular classification. Methods We reviewed 240 EC specimens from our hospital database. A ddPCR assay was used to identify POLE mutations at 5 known hotspots (P286R, S297F, V411L, A456P, and S459F). Expressions of p53 and mismatch repair proteins were identified using immunohistochemistry. Results The ddPCR assay identified POLE mutations in 10.8% of patients. The most common mutation was V411L (61.54%), followed by P286R (23.07%), S459F (7.69%), S297F (3.85%), and A456P (3.85%). Eight/one cases had positive ddPCR but negative Sanger sequencing/next-generation sequencing, respectively. Molecular classification revealed p53-mutated subtype as significantly more common for tumors with a high International Federation of Gynecology and Obstetrics (FIGO) grade, deep myometrial invasion, lymphovascular space invasion, advanced stage, and high/advanced risk groups; the POLE mutated group was more frequent in the low stage and low/intermediate risk group. Survival analyses revealed the poorest outcomes for p53-mutated EC, while mismatch repair-deficient and no specific molecular profile ECs had similar progression-free survival (PFS) outcomes, and POLE-mutated ECs had the best PFS outcome (p<0.001). When only intermediate, high-intermediate, and high-risk groups were analyzed for subgroups, molecular classification still showed differences both in PFS (p=0.003) and overall survival (p=0.017). Conclusion Hotspot POLE mutations can be detected using the ddPCR assay. We suggest simultaneously evaluating POLE mutation status using ddPCR and p53/mismatch repair protein expressions using immunohistochemistry, which can rapidly and accurately determine the molecular subtype of EC. Using droplet digital polymerase chain reaction (ddPCR), we successfully detected the 5 most frequent pathogenic hotspot mutations in the POLE gene in samples from endometrial cancer patients, thus confirming the utility of ddPCR in their identification.
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Affiliation(s)
- Gilhyang Kim
- Department of Pathology, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
| | - Song Kook Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Dong Hoon Suh
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Kidong Kim
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jae Hong No
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Yong Beom Kim
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Hyojin Kim
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea.
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13
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Kim B, Nam SK, Seo SH, Park KU, Ahn SH, Park DJ, Kim HH, Kim WH, Lee HS. Comparative analysis of HER2 copy number between plasma and tissue samples in gastric cancer using droplet digital PCR. Sci Rep 2020; 10:4177. [PMID: 32144300 PMCID: PMC7060190 DOI: 10.1038/s41598-020-60897-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/17/2020] [Indexed: 01/18/2023] Open
Abstract
In this study, we measured the human epidermal growth factor receptor 2 (HER2) copy number in both tissue and plasma samples of gastric cancer patients by using droplet digital polymerase chain reaction (ddPCR) method. Eighty gastric cancer patients were enrolled and both formalin-fixed and paraffin-embedded tissue and preoperative plasma samples were collected. HER2 status was determined by HER2 immunohistochemistry (IHC)/silver in situ hybridization (SISH) in tissue samples and ddPCR of the target gene HER2 and the reference gene eukaryotic translation initiation factor 2C, 1 in both tissue and plasma. The concordance rate of tissue HER2 status determined by IHC/SISH and HER2 ddPCR was 90.0% (72/80), and the sensitivity and specificity of tissue ddPCR were 85.0% and 95.0%, respectively. The concordance rate of plasma ddPCR and IHC/SISH was 63.8% (51/80). The sensitivity, specificity, positive predictive value, and negative predictive value of plasma HER2 ddPCR were 37.5%, 90.0%, 79.0%, and 59.0%, respectively. As HER2 measurement by tissue ddPCR showed a high concordance rate with HER2 status by IHC/SISH, it could replace tissue IHC/SISH testing in gastric cancer. These findings may contribute to the development of tissue and plasma HER2 testing that would be useful in daily practice.
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Affiliation(s)
- Boram Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Soo Kyung Nam
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Sang-Hoon Ahn
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.,Department of Surgery, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Do Joong Park
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Hyung-Ho Kim
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.,Department of Surgery, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea. .,Department of Pathology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
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14
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Marchiò C, Annaratone L, Marques A, Casorzo L, Berrino E, Sapino A. Evolving concepts in HER2 evaluation in breast cancer: Heterogeneity, HER2-low carcinomas and beyond. Semin Cancer Biol 2020; 72:123-135. [PMID: 32112814 DOI: 10.1016/j.semcancer.2020.02.016] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/16/2020] [Accepted: 02/22/2020] [Indexed: 02/06/2023]
Abstract
The human epidermal growth factor receptor 2 (HER2) is a well-known negative prognostic factor in breast cancer and a target of the monoclonal antibody trastuzumab as well as of other anti-HER2 compounds. Pioneering works on HER2-positive breast cancer in the 90s' launched a new era in clinical research and oncology practice that has reshaped the natural history of this disease. In diagnostic pathology the HER2 status is routinely assessed by using a combination of immunohistochemistry (IHC, to evaluate HER2 protein expression levels) and in situ hybridization (ISH, to assess HER2 gene status). For this purpose, international recommendations have been developed by a consensus of experts in the field, which have changed over the years according to new experimental and clinical data. In this review article we will document the changes that have contributed to a better evaluation of the HER2 status in clinical practice, furthermore we will discuss HER2 heterogeneity defined by IHC and ISH as well as by transcriptomic analysis and we will critically describe the complexity of HER2 equivocal results. Finally, we will introduce the clinical impact of HER2 mutations and we will define the upcoming category of HER2-low breast cancer with respect to emerging clinical data on the efficacy of specific anti-HER2 agents in subgroups of breast carcinomas lacking the classical oncogene addition dictated by HER2 amplification.
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Affiliation(s)
- Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin, Italy; Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Turin, Italy; Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Ana Marques
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy; Pathology Unit, Centro Hospitalar São João, Porto, Portugal
| | - Laura Casorzo
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy; Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy; Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.
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15
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Bae JM, Wen X, Kim TS, Kwak Y, Cho NY, Lee HS, Kang GH. Fibroblast Growth Factor Receptor 1 (FGFR1) Amplification Detected by Droplet Digital Polymerase Chain Reaction (ddPCR) Is a Prognostic Factor in Colorectal Cancers. Cancer Res Treat 2020; 52:74-84. [PMID: 31096734 PMCID: PMC6962468 DOI: 10.4143/crt.2019.062] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/07/2019] [Indexed: 01/06/2023] Open
Abstract
PURPOSE The purpose of this study was to reveal the clinicopathological characteristics and prognostic implications associated with fibroblast growth factor receptor 1 (FGFR1) amplification in colorectal cancers (CRCs). MATERIALS AND METHODS We measured the copy number of FGFR1 by droplet digital polymerase chain reaction (ddPCR), and analyzed the FGFR1 expression by immunohistochemistry, in 764 surgically resected CRCs (SNUH2007 dataset, 384 CRCs; SNUH Folfox dataset, 380 CRCs). RESULTS CRCs with ≥ 3.3 copies of the FGFR1 gene were classified as FGFR1 amplified. FGFR1 amplification was found in 10 of the 384 CRCs (2.6%) in the SNUH2007 dataset, and in 28 of the 380 CRCs (7.4%) in the SNUH Folfox dataset. In the SNUH2007 dataset, there was no association between the FGFR1 copy number status and sex, gross appearance, stage, or differentiation. High FGFR1 expression was associated with female sex and KRAS mutation. At the molecular level, FGFR1 amplification was mutually exclusive with BRAF mutation, microsatellite instability, and MLH1 methylation, in both SNUH2007 and SNUH Folfox datasets. Survival analysis revealed that FGFR1 amplification was associated with significantly worse clinical outcome compared with no FGFR1 amplification, in both SNUH2007 and SNUH Folfox datasets. Within the SNUH2007 dataset, CRC patients with high FGFR1 expression had an inferior progression-free survival compared with those with low FGFR1 expression. The FGFR inhibitor, PD173074, repressed the proliferation of a CRC cell line overexpressing FGFR1, but not of cells with FGFR1 amplification. CONCLUSION FGFR1 amplification measured by ddPCR can be a prognostic indicator of poor clinical outcome in patients with CRCs.
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Affiliation(s)
- Jeong Mo Bae
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Xianyu Wen
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Tae-Shin Kim
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Yoonjin Kwak
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Nam-Yun Cho
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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16
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Suryavanshi M, Jaipuria J, Mehta A, Kumar D, Panigrahi MK, Verma H, Saifi M, Sharma S, Tandon S, Doval DC, Das BC. Droplet digital polymerase chain reaction offers an improvisation over conventional immunohistochemistry and fluorescent in situ hybridization for ascertaining Her2 status of breast cancer. South Asian J Cancer 2019; 8:203-210. [PMID: 31807475 PMCID: PMC6852626 DOI: 10.4103/sajc.sajc_344_18] [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] [Indexed: 11/04/2022] Open
Abstract
Background Droplet digital polymerase chain reaction (DDPCR) is a recent modality for detecting Her2 expression which is quantitative, cheaper, easier to standardize, and free from interobserver variation. Purpose The purpose of this study is to incorporate DDPCR in the current diagnostic paradigm with clinical benefit. Materials and Methods Fifty-four consecutive patients were tested by immunohistochemistry (IHC), fluorescent in situ hybridization (FISH), and DDPCR. With FISH result as gold standard, receiver operating characteristic curves for DDPCR ratio were analyzed to label Her2-negative, equivocal, and positive cases as DDPCR score 1, 2, and 3, respectively. Proportion of patients labeled unequivocally as Her2 positive or negative was defined to have "clinically benefitted" from the test. Drawing parallel to inter-relationships between DDPCR, IHC, and FISH in the test cohort, four diagnostic pathways were defined - (1) initial IHC followed by FISH, (2) initial DDPCR followed by FISH, (3) initial IHC followed by DDPCR followed by FISH, and (4) initial DDPCR followed by IHC followed by FISH. Results Clinical benefit of DDPCR as an initial test in the test cohort was 57%, while it was 65% if used as a second-line test among those with an initial inconclusive IHC result. Sensitivity analysis in the simulation cohort revealed that if DDPCR cost was ≤0.6 times the cost of IHC, then a three-step pathway with DDPCR upfront would near certainly prove most cost beneficial. If DDPCR cost was >0.6 but ≤2 times the cost of IHC, then a three-step pathway with DDPCR as second-line test had a higher probability to prove most cost beneficial. If DDPCR cost was >2 times the cost of IHC, then conventional pathway had a higher probability to prove most cost-effective. Conclusion Incorporating DDPCR in the current clinical diagnostic paradigm has the potential to improve its cost-effectiveness and benefit.
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Affiliation(s)
| | - Jiten Jaipuria
- Department of Urogynaeoncology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Anurag Mehta
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Dushyant Kumar
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | | | - Haristuti Verma
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Mumtaz Saifi
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Sanjeev Sharma
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Simran Tandon
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, Uttar Pradesh, India
| | | | - Bhudev C Das
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, Uttar Pradesh, India
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17
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Sakai K, Maeda S, Saeki K, Yoshitake R, Goto-Koshino Y, Nakagawa T, Nishimura R, Yonezawa T, Matsuki N. ErbB2 Copy Number Aberration in Canine Urothelial Carcinoma Detected by a Digital Polymerase Chain Reaction Assay. Vet Pathol 2019; 57:56-65. [PMID: 31640537 DOI: 10.1177/0300985819879445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Urothelial carcinoma (UC) is the most common tumor affecting the urinary bladder of dogs. Protein overexpression of ErbB2 (the canine homolog of HER2) has been observed in dogs with UC. However, no study regarding ErbB2 copy number aberration (CNA) is reported in dogs with UC. In this study, a digital PCR assay for detecting CNA of canine ErbB2 was developed. DNA samples were isolated from 83 formalin-fixed, paraffin-embedded urinary bladder tissues (36 UC, 8 polypoid cystitis, and 39 normal) and 94 urinary sediments (54 UC, 30 nonneoplastic, and 10 normal). The copy number of canine chromosome 8 (CFA8) was used as a control. In the urinary bladder tissues, ErbB2 CNA was detected in 12 of 36 (33%) UC, 2 of 8 (25%) polypoid cystitis, and 0 of 39 (0%) normal controls. In the urinary sediments, ErbB2 CNA was also detected in 19 of 54 (35%) UC; however, no ErbB2 CNA was detected in nonneoplastic diseases or normal controls. The sensitivity and specificity of ErbB2 CNA in urinary sediment for the detection of UC were 35% and 100%, respectively. There was a positive correlation between the copy number ratios of ErbB2 to CFA8 in the urinary bladder tissues and urinary sediments. Our findings indicate that the digital PCR assay of urinary sediments may be a useful, noninvasive method for detecting ErbB2 CNA in dogs with UC.
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Affiliation(s)
- Kosei Sakai
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shingo Maeda
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kohei Saeki
- Department of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryohei Yoshitake
- Department of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuko Goto-Koshino
- Molecular Diagnostic Laboratory, Veterinary Medical Center, The University of Tokyo, Tokyo, Japan
| | - Takayuki Nakagawa
- Department of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryohei Nishimura
- Department of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Yonezawa
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Naoaki Matsuki
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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18
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Hamdan D, Nguyen TT, Leboeuf C, Meles S, Janin A, Bousquet G. Genomics applied to the treatment of breast cancer. Oncotarget 2019; 10:4786-4801. [PMID: 31413819 PMCID: PMC6677666 DOI: 10.18632/oncotarget.27102] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/05/2019] [Indexed: 12/20/2022] Open
Abstract
Breast cancer remains a major health issue in the world with 1.7 million new cases in 2012 worldwide. It is the second cause of death from cancer in western countries. Genomics have started to modify the treatment of breast cancer, and the developments should become more and more significant, especially in the present era of treatment personalization and with the implementation of new technologies. With molecular signatures, genomics enabled a de-escalation of chemotherapy and personalized treatments of localized forms of estrogen-dependent breast cancers. Genomics can also make a real contribution to constitutional genetics, so as to identify mutations in a panel of candidate genes. In this review, we will discuss the contributions of genomics applied to the treatment of breast cancer, whether already validated contributions or possible future applications linked to research data.
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Affiliation(s)
- Diaddin Hamdan
- Hôpital La Porte Verte, Versailles F-78004, France.,U942, Université Paris-Diderot, INSERM, Paris F-75010, France
| | - Thi Thuy Nguyen
- U942, Université Paris-Diderot, INSERM, Paris F-75010, France.,National Cancer Hospital, Medical Oncology Department 2, Ha Noi 110000, Viet Nam.,Ha Noi Medical University, Oncology Department, Ha Noi 116001, Viet Nam
| | - Christophe Leboeuf
- U942, Université Paris-Diderot, INSERM, Paris F-75010, France.,AP-HP-Hôpital Saint-Louis, Laboratoire de Pathologie, Paris F-75010, France
| | - Solveig Meles
- U942, Université Paris-Diderot, INSERM, Paris F-75010, France
| | - Anne Janin
- U942, Université Paris-Diderot, INSERM, Paris F-75010, France.,AP-HP-Hôpital Saint-Louis, Laboratoire de Pathologie, Paris F-75010, France
| | - Guilhem Bousquet
- U942, Université Paris-Diderot, INSERM, Paris F-75010, France.,AP-HP-Hôpital Avicenne, Service d'Oncologie Médicale, Bobigny F-93000, France.,Université Paris 13, Leonard de Vinci, Villetaneuse F-93430, France
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19
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Lee KS, Nam SK, Seo SH, Park KU, Oh HK, Kim DW, Kang SB, Kim WH, Lee HS. Digital polymerase chain reaction for detecting c-MYC copy number gain in tissue and cell-free plasma samples of colorectal cancer patients. Sci Rep 2019; 9:1611. [PMID: 30733532 PMCID: PMC6367402 DOI: 10.1038/s41598-018-38415-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/28/2018] [Indexed: 02/07/2023] Open
Abstract
We focused on the utility of the droplet digital polymerase chain reaction (ddPCR) for detecting c-MYC gene copy number (GCN) gain in cell-free plasma and tumor tissue of colorectal cancer (CRC) patients. c-MYC GCN status was determined using dual-color silver in situ hybridization (SISH) and ddPCR in retrospective cohort 1 (192 CRC patients) and prospective cohort 2 (64 CRC patients). In cohort 1, c-MYC GCN gain was observed in 34 (17.5%) patients by SISH, and in 7 (3.6%) patients by ddPCR. c-MYC GCN by SISH significantly correlated with ddPCR results (ρ = 0.532, P < 0.001). Although 40 cases (20.7%) showed intratumoral genetic heterogeneity, it did not cause discordance in results obtained by the two methods. c-MYC GCN gain, by both SISH and ddPCR was independently correlated with worst prognosis (P = 0.002). In cohort 2, c-MYC GCN estimation in tissue by ddPCR was also significantly associated with results obtained by SISH (ρ = 0.349, P = 0.005), but correlated with plasma ddPCR with borderline significance (ρ = 0.246, P = 0.050). Additionally, detecting c-MYC GCN gain in plasma with ddPCR might have relatively low sensitivity but high specificity. Our study suggests that ddPCR can be a useful tool for detecting c-MYC GCN gain as a potential prognostic biomarker in CRC tissue samples; however, this will need further verification in plasma samples.
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Affiliation(s)
- Kyu Sang Lee
- Department of Pathology, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Soo Kyung Nam
- Department of Pathology, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Heung-Kwon Oh
- Department of Surgery, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-707, Republic of Korea
| | - Duck-Woo Kim
- Department of Surgery, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-707, Republic of Korea
| | - Sung-Bum Kang
- Department of Surgery, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-707, Republic of Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea. .,Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
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20
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Somasundaram DB, Aravindan S, Yu Z, Jayaraman M, Tran NTB, Li S, Herman TS, Aravindan N. Droplet digital PCR as an alternative to FISH for MYCN amplification detection in human neuroblastoma FFPE samples. BMC Cancer 2019; 19:106. [PMID: 30691436 PMCID: PMC6348625 DOI: 10.1186/s12885-019-5306-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/16/2019] [Indexed: 11/17/2022] Open
Abstract
Background MYCN amplification directly correlates with the clinical course of neuroblastoma and poor patient survival, and serves as the most critical negative prognostic marker. Although fluorescence in situ hybridization (FISH) remains the gold standard for clinical diagnosis of MYCN status in neuroblastoma, its limitations warrant the identification of rapid, reliable, less technically challenging, and inexpensive alternate approaches. Methods In the present study, we examined the concordance of droplet digital PCR (ddPCR, in combination with immunohistochemistry, IHC) with FISH for MYCN detection in a panel of formalin-fixed paraffin-embedded (FFPE) human neuroblastoma samples. Results In 112 neuroblastoma cases, ddPCR analysis demonstrated a 96–100% concordance with FISH. Consistently, IHC grading revealed 92–100% concordance with FISH. Comparing ddPCR with IHC, we observed a concordance of 95–98%. Conclusions The results demonstrate that MYCN amplification status in NB cases can be assessed with ddPCR, and suggest that ddPCR could be a technically less challenging method of detecting MYCN status in FFPE specimens. More importantly, these findings illustrate the concordance between FISH and ddPCR in the detection of MYCN status. Together, the results suggest that rapid, less technically demanding, and inexpensive ddPCR in conjunction with IHC could serve as an alternate approach to detect MYCN status in NB cases, with near-identical sensitivity to that of FISH.
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Affiliation(s)
- Dinesh Babu Somasundaram
- Departments of Radiation Oncology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, OK, 73104, USA
| | | | - Zhongxin Yu
- Department of Pathology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, BMSB 451, Oklahoma City, OK, 73104, USA
| | - Muralidharan Jayaraman
- Stephenson Cancer Center, Oklahoma City, OK, USA.,Department of Cell Biology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, BMSB 553, Oklahoma City, OK, 73104, USA
| | - Ngoc T B Tran
- Department of Pathology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, BMSB 451, Oklahoma City, OK, 73104, USA
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, 1200 Children's Ave. Ste 14000, Oklahoma City, OK, 73104, USA
| | - Terence S Herman
- Departments of Radiation Oncology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, OK, 73104, USA.,Stephenson Cancer Center, Oklahoma City, OK, USA
| | - Natarajan Aravindan
- Departments of Radiation Oncology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, OK, 73104, USA. .,Department of Pathology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, BMSB 451, Oklahoma City, OK, 73104, USA. .,Department of Anesthesiology, University of Oklahoma Health Sciences Center, 920 SL Young Blvd #1140, Oklahoma City, OK, 73104-5036, USA.
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21
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Droplet digital PCR revealed high concordance between primary tumors and lymph node metastases in multiplex screening of KRAS mutations in colorectal cancer. Clin Exp Med 2019; 19:219-224. [PMID: 30661213 DOI: 10.1007/s10238-019-00545-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
Abstract
The proto-oncogene KRAS belongs among the most frequently mutated genes in all types of cancer and is also very important oncogene related to colorectal tumors. The detection of mutations in this gene in primary tumor is a predictive biomarker for the anti-EGFR therapy in metastatic CRC (mCRC); however, the patients with wild-type KRAS can also show resistance to the personalized medicine. The droplet-based digital PCR technology has improved the analytical sensitivity of the mutations detection, which led us to the idea about the optimization of this approach for KRAS testing. In this study, we report the application of ddPCR technology in order to analyze the presence of KRAS mutations in primary tumor and matched metastasis in lymph nodes (LNs) from patients with mCRC and address the question, whether the improvement in the detection method can lower the discrepancies of KRAS mutations detection between the primary tumor and regional LNs. Genomic DNA with wtKRAS and commercial DNA with mtKRAS (G12D) were used to set up the ddPCR reaction. Formalin-fixed paraffin-embedded tissues from primary tumor and positive lymph node from 31 patients with mCRC were analyzed using ddPCR and Sanger sequencing. KRAS status of primary tumors was known; however, the mutation status of lymph nodes was not detected previously. From 31 samples of primary tumors, our results corresponded to results from IVD kit in 30 cases. For one patient, ddPCR detected KRAS mutation in comparison with negative result of the IVD kit. In the samples of metastatic infiltrated LNs, ddPCR detected 16 samples as a WT KRAS and 15 lymph nodes showed positivity for KRAS mutation, whereby Sanger sequencing found KRAS mutations in 8 cases only. We also found two cases where genetic conditions of KRAS gene differed between primary tumor and infiltrated lymph node, both "low-grade" adenocarcinoma. Our study approved that ddPCR method is adequate technique with high sensitivity and in the future may be used as a diagnostic tool for evaluation of KRAS mutations, especially in infiltrated LNs of patients with mCRC.
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22
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Tantiwetrueangdet A, Panvichian R, Wongwaisayawan S, Sueangoen N, Lertsithichai P. Droplet digital PCR using HER2/EIF2C1 ratio for detection of HER2 amplification in breast cancer tissues. Med Oncol 2018; 35:149. [PMID: 30284063 PMCID: PMC6182624 DOI: 10.1007/s12032-018-1210-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/26/2018] [Indexed: 01/03/2023]
Abstract
Breast cancers with amplification and overexpression of human epithelial growth factor receptor 2 (HER2) are associated with poor prognosis, and targeted for anti-HER2 therapy. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are currently the recommended methods to asses HER2 overexpression/amplification. Droplet digital PCR (ddPCR), a highly accurate method to quantify DNA copy number, is potentially a robust alternative for HER2 diagnostics. In the FISH assay and most of previous ddPCR reports, chromosome 17 centromere (CEP17) has been used as the reference control to determine HER2/CEP17 ratio. Nevertheless, miss-classification could occur when HER2 is co-amplified with CEP17. To avoid this inherent defect, in the present study, we employed ddPCR assay using the human eukaryotic translation initiation factor 2C1 (EIF2C1) gene located at chromosome 1p34.3 as the reference control to quantify HER2 copy number in 31 frozen breast cancer tissues. HER2 status of these samples had been determined by FISH and classified as HER2-amplified and HER2-non-amplified breast cancers. The results showed that HER2 determined by ddPCR using HER2/EIF2C1 ratio was in good concordance with HER2 determined by FISH using HER2/CEP17 ratio, the concordance rate 87.1% (27/31), Kappa = 0.719. The sensitivity and specificity of ddPCR assay was 90% (9/10) and 85.7% (18/21), respectively. The median HER2/EIF2C1 copy number ratio in HER2-amplified cancers (6.55, range 1.3–17.3) was significantly higher than in HER2-non-amplified cancers (1.05, range 0.6–3.6, p < 0.001). This study demonstrated that ddPCR using HER2/EIF2C1 ratio could accurately assess HER2 status in frozen breast cancer tissues. Thus, our findings warrant further studies into breast cancer with HER2-equivocal by IHC/FISH.
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Affiliation(s)
| | - Ravat Panvichian
- Department of Internal Medicine, Division of Medical Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Rama 6 Road, Rajthevi, Bangkok, 10400 Thailand
| | - Sansanee Wongwaisayawan
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Natthaporn Sueangoen
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Panuwat Lertsithichai
- Department of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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23
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Denis JA, Guillerm E, Coulet F, Larsen AK, Lacorte JM. The Role of BEAMing and Digital PCR for Multiplexed Analysis in Molecular Oncology in the Era of Next-Generation Sequencing. Mol Diagn Ther 2018; 21:587-600. [PMID: 28667577 DOI: 10.1007/s40291-017-0287-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BEAMing polymerase chain reaction (PCR) and digital PCR (dPCR) are used for robust and accurate quantification of nucleic acids. These methods are particularly well suited for the identification of very small fractions (<1%) of variant copies such as the presence of mutant genes in a predominantly wild-type background. BEAMing and dPCR are increasingly used in diverse fields including bacteriology, virology, non-invasive prenatal testing, and oncology, in particular for the molecular analysis of liquid biopsies. In this review, we present the principles of BEAMing and dPCR as well as the trends of future technical development, focusing on the possibility of developing multiplexed mutation analysis. Finally, we will discuss why such techniques will remain useful despite the ever-decreasing costs and increased automatization of next-generation sequencing (NGS), using molecular characterization of cancer cells as an example.
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Affiliation(s)
- Jérôme Alexandre Denis
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France. .,Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine, INSERM, UMRS 938, 75571, Paris Cedex 12, France. .,Department of Endocrine and Oncological Biochemistry, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris, France.
| | - Erell Guillerm
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMRS 938 Centre de Recherche Saint-Antoine, "Instability of Microsatellites and Cancers", Team approved by the National League Against Cancer, 75571, Paris Cedex 12, France.,Departement of Genetics, Unit of Molecular Oncogenetics and Angiogenetics, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris Cedex, France
| | - Florence Coulet
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMRS 938 Centre de Recherche Saint-Antoine, "Instability of Microsatellites and Cancers", Team approved by the National League Against Cancer, 75571, Paris Cedex 12, France.,Departement of Genetics, Unit of Molecular Oncogenetics and Angiogenetics, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris Cedex, France
| | - Annette K Larsen
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine, INSERM, UMRS 938, 75571, Paris Cedex 12, France
| | - Jean-Marc Lacorte
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMR_S 1166, Research Institute of Cardiovascular Disease, Metabolism and Nutrition, 75013, Paris, France.,Department of Endocrine and Oncological Biochemistry, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris, France
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24
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Elbouchtaoui M, Tengher I, Miquel C, Brugière C, Benbara A, Zelek L, Ziol M, Bouhidel F, Janin A, Bousquet G, Leboeuf C. Micromolecular methods for diagnosis and therapeutic strategy: a case study. Oncotarget 2018; 9:22862-22869. [PMID: 29854320 PMCID: PMC5978270 DOI: 10.18632/oncotarget.25161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 04/03/2018] [Indexed: 01/04/2023] Open
Abstract
An intraductal carcinoma, 55 mm across, was diagnosed on a total mastectomy in a 45-year-old woman. The 2 micro-invasive areas found were too small for reliable immunostainings for estrogen, progesterone, and HER2 receptors. In the sentinel lymph-node, a subcapsular tumor embole of about 50 cancer cells was identified on the extemporaneous cryo-cut section, but not on further sections after paraffin-embedding of the sample. Considering this tumor metastatic potential, we decided to assess HER2 status on the metastatic embole using pathological and molecular micro-methods. We laser-microdissected the tumor cells, extracted their DNA, and performed droplet-digital-PCR (ddPCR) for HER2 gene copy number variation. The HER2/RNaseP allele ratio was 5.2 in the laser-microdissected tumor cells, similar to the 5.3 ratio in the HER2-overexpressing breast cancer cell line BT-474. We thus optimized the adjuvant treatment of our patient and she received a trastuzumab-based adjuvant chemotherapy.
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Affiliation(s)
- Morad Elbouchtaoui
- Université Paris Diderot, Inserm, UMR_S1165, Paris, France.,Pathology Department, Hôpital St Louis, APHP, Paris, France
| | - Iulia Tengher
- Pathology Department, Hôpital Jean Verdier, APHP, Bondy, France
| | - Catherine Miquel
- Université Paris Diderot, Inserm, UMR_S1165, Paris, France.,Pathology Department, Hôpital St Louis, APHP, Paris, France
| | | | - Amélie Benbara
- Obstetrics and Gynecology Department, Hôpital Jean Verdier, APHP, Bondy, France
| | - Laurent Zelek
- Université Paris 13, Villetaneuse, France.,Oncology Department, Hôpital Avicenne, APHP, Bobigny, France
| | - Marianne Ziol
- Pathology Department, Hôpital Jean Verdier, APHP, Bondy, France.,Université Paris 13, Villetaneuse, France.,Inserm UMR_S1162, Paris, France
| | - Fatiha Bouhidel
- Université Paris Diderot, Inserm, UMR_S1165, Paris, France.,Pathology Department, Hôpital St Louis, APHP, Paris, France
| | - Anne Janin
- Université Paris Diderot, Inserm, UMR_S1165, Paris, France.,Pathology Department, Hôpital St Louis, APHP, Paris, France
| | - Guilhem Bousquet
- Université Paris Diderot, Inserm, UMR_S1165, Paris, France.,Université Paris 13, Villetaneuse, France.,Oncology Department, Hôpital Avicenne, APHP, Bobigny, France
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25
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Christgen M, van Luttikhuizen JL, Raap M, Braubach P, Schmidt L, Jonigk D, Feuerhake F, Lehmann U, Schlegelberger B, Kreipe HH, Steinemann D. Precise ERBB2 copy number assessment in breast cancer by means of molecular inversion probe array analysis. Oncotarget 2018; 7:82733-82740. [PMID: 27716627 PMCID: PMC5347728 DOI: 10.18632/oncotarget.12421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 09/19/2016] [Indexed: 01/01/2023] Open
Abstract
HER2/ERBB2 amplification/overexpression determines the eligibility of breast cancer patients to HER2-targeted therapy. This study evaluates the agreement between ERBB2 copy number assessment by fluorescence in situ hybridization, a standard method recommended by the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP), and newly available DNA extraction-based methods. A series of n=29 formalin-fixed paraffin-embedded breast cancers were subjected to ERBB2 copy number assessment by fluorescence in situ hybridization (FISH, Vysis, Abbott). Following macrodissection of invasive breast cancer tissue and DNA extraction, ERBB2 copy number was also determined by molecular inversion probe array analysis (MIP, OncoScan, Affymetrix) and next generation sequencing combined with normalized amplicon coverage analysis (NGS/NAC, AmpliSeq, Ion Torrent). ERBB2 copy number values obtained by MIP or NGS/NAC were tightly correlated with ERBB2 copy number values obtained by conventional FISH (rs = 0.940 and rs = 0.894, P < 0.001). Using ASCO/CAP guideline-conform thresholds for categorization of breast cancers as HER2-negative, equivocal or positive, nearly perfect concordance was observed for HER2 classification by FISH and MIP (93% concordant classifications, κ = 0.87). Substantial concordance was observed for FISH and NGS/NAC (83% concordant classifications, κ = 0.62). In conclusion, MIP facilitates precise ERBB2 copy number detection and should be considered as an ancillary method for clinical HER2 testing.
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Affiliation(s)
| | | | - Mieke Raap
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Peter Braubach
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Lars Schmidt
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | | | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | | | - Hans H Kreipe
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
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26
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Monico J, Miller B, Rezeanu L, May W, Sullivan DC. Fibroblast growth factor receptor 1 amplification in laryngeal squamous cell carcinoma. PLoS One 2018; 13:e0186185. [PMID: 29351293 PMCID: PMC5774678 DOI: 10.1371/journal.pone.0186185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/26/2017] [Indexed: 12/17/2022] Open
Abstract
Fibroblast growth factor receptor 1 (FGFR1) has been noted to be amplified in a variety of squamous cell carcinomas (SCCa) of the head, neck, and lung and increased copy number (CN) is a predictor of poor outcomes. FGFR1 is a therapeutic target for lung SCCa and inhibition therapy is currently in clinical trials. Absolute quantification of FGFR1 from formalin fixed paraffin embedded (FFPE) tissue of laryngeal SCCa was examined in this retrospective study. A droplet digital polymerase chain reaction (ddPCR) was used for absolute quantitation of the FGFR1 gene CN. Of the 74 samples analyzed, FGFR1 CN analysis revealed 54% of samples had CN greater than 2 copies/cell (1.8-2.2 copies/cell), and 38% had CN values greater than 3. The mean and standard deviation FGFR1 CN was 4.17 ± 1.46 CN for African American patients (n = 41) and 3.78 ±1.85 CN for Caucasian patients (n = 31). Further, 60.9% of specimens from African Americans demonstrated increased FGFR1 CN compared to 48.4% of Caucasians. Two SCCA samples from Native American demonstrated increased FGFR1 CN (4.19 and 3.01 CN). The level of FGFR1 amplification did not correlate with tumor stage, lymph node staging, or metastasis. In this population, the proportion of patient samples with an FGFR1 amplification was three times higher than in reported for SCCA of the head and neck. Further, increased FGFR1 CN was observed in two racial groups not previously reported: African Americans and Native Americans. However, FGFR1 amplification is not prognostic in laryngeal squamous cell carcinomas.
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Affiliation(s)
- Jesus Monico
- Department of Pathology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Brandon Miller
- Department of Otolaryngology and Communicative Sciences, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Luminita Rezeanu
- Department of Pathology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Warren May
- Department of Biostatistics, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Donna C. Sullivan
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
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27
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Robust and accurate digital measurement for HER2 amplification in HER2 equivocal breast cancer diagnosis. Sci Rep 2017; 7:6752. [PMID: 28754904 PMCID: PMC5533703 DOI: 10.1038/s41598-017-07176-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/21/2017] [Indexed: 11/09/2022] Open
Abstract
Currently, there are no recommended alternative assays for HER2 cases deemed equivocal by immunohistochemistry and fluorescent in situ hybridization. Digital PCR (ddPCR), a highly accurate method to determine DNA copy number, could be a robust alternative for clinical HER2 diagnostics. HER2 and CEP17 copy numbers were quantified using two ddPCR platforms (QX200 and RainDrop) in 102 samples of invasive breast cancers. Compared to routine assays, ddPCR gave a sensitivity and specificity of 82.8% and 97.3% respectively, with a kappa value of 0.833 (p < 0.001). Moreover, the method proved to be robust as the results from two platforms was highly correlated (R2 = 0.91; Concordance rate = 97%; κ = 0.923, P < 0.001). Its performance was further tested on 114 HER2 equivocal cases in an independent validation cohort. 75% (21/28) of cases with HER2 amplification and 95% (82/86) of HER2 non-amplified case were classified as positive and negative by ddPCR respectively (κ = 0.709, P < 0.001). Notably, in the HER2 amplified cases, a lower percentage of HER2 positive cells could be related to the discordant results. Altogether, ddPCR is a robust alternative for clinical HER2 diagnostics. However, intratumoral heterogeneity of HER2 status still pose a challenge for HER2 analysis by ddPCR.
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28
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Lodrini M, Sprüssel A, Astrahantseff K, Tiburtius D, Konschak R, Lode HN, Fischer M, Keilholz U, Eggert A, Deubzer HE. Using droplet digital PCR to analyze MYCN and ALK copy number in plasma from patients with neuroblastoma. Oncotarget 2017; 8:85234-85251. [PMID: 29156716 PMCID: PMC5689606 DOI: 10.18632/oncotarget.19076] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/20/2017] [Indexed: 01/28/2023] Open
Abstract
The invasive nature of surgical biopsies deters sequential application, and single biopsies often fail to reflect tumor dynamics, intratumor heterogeneity and drug sensitivities likely to change during tumor evolution and treatment. Implementing molecular characterization of cell-free neuroblastoma-derived DNA isolated from blood plasma could improve disease assessment for treatment selection and monitoring of patients with high-risk neuroblastoma. We established droplet digital PCR (ddPCR) protocols for MYCN and ALK copy number status in plasma from neuroblastoma patients. Our ddPCR protocol accurately discriminated between MYCN and ALK amplification, gain and normal diploid status in a large panel of neuroblastoma cell lines, and discrepancies with reported MYCN and ALK status were detected, including a high-level MYCN amplification in NB-1, a MYCN gain in SH-SY5Y, a high-level ALK amplification in IMR-32 and ALK gains in BE(2)-C, Kelly, SH-SY5Y and LAN-6. MYCN and ALK status were also reliably determined from cell-free DNA derived from medium conditioned by the cell lines. MYCN and ALK copy numbers of subcutaneous neuroblastoma xenograft tumors were accurately determined from cell-free DNA in the mouse blood plasma. In a final validation step, we accurately distinguished MYCN and ALK copy numbers of the corresponding primary tumors using retrospectively collected blood plasma samples from 10 neuroblastoma patients. Our data justify the further development of molecular disease characterization using cell-free DNA in blood plasma from patients with neuroblastoma. This expanded molecular diagnostic palette may improve monitoring of disease progression including relapse and metastatic events as well as therapy success or failure in high-risk neuroblastoma patients.
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Affiliation(s)
- Marco Lodrini
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Sprüssel
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Kathy Astrahantseff
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Daniela Tiburtius
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Robert Konschak
- Translational Radiation Oncology Research Laboratory, Department of Radiooncology and Radiotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
| | - Holger N Lode
- Department of Pediatric Hematology and Oncology, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, Germany
| | - Matthias Fischer
- Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Hedwig E Deubzer
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,Junior Neuroblastoma Research Group, Experimental and Clinical Research Center (ECRC), Berlin, Germany
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30
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Ålgars A, Sundström J, Lintunen M, Jokilehto T, Kytölä S, Kaare M, Vainionpää R, Orpana A, Österlund P, Ristimäki A, Carpen O, Ristamäki R. EGFR gene copy number predicts response to anti-EGFR treatment in RAS wild type and RAS/BRAF/PIK3CA wild type metastatic colorectal cancer. Int J Cancer 2016; 140:922-929. [PMID: 27879995 DOI: 10.1002/ijc.30507] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 09/15/2016] [Accepted: 10/05/2016] [Indexed: 12/17/2022]
Abstract
Anti-EGFR antibodies are used for the treatment of RAS wild type metastatic colorectal cancer. We previously showed that EGFR gene copy number (GCN) predicts response to anti-EGFR therapy in KRAS exon 2 wild type metastatic colorectal cancer. The aim of our study was to analyse the predictive role of EGFR GCN in RAS/BRAF/PIK3CA wild type metastatic colorectal cancer. The material included 102 patients with KRAS exon 2 wild type metastatic colorectal cancer treated with anti-EGFR ± cytotoxic therapy. Next generation sequencing was used for KRAS, NRAS, BRAF and PIK3CA gene mutation analyses. EGFR GCN was analysed by EGFR immunohistochemistry guided automated silver in situ hybridisation. Increased EGFR GCN (≥4.0) predicted a better response and prolonged progression free survival in anti-EGFR treated RAS/BRAF/PIK3CA wild type patients (Log-rank test, p = 0.0004). In contrast, survival of RAS/BRAF/PIK3CA wild type, EGFR GCN below 4.0 patients did not differ from patients with mutant RAS, BRAF or PIK3CA. Our study indicates that EGFR GCN predicts anti-EGFR treatment efficacy in patients with RAS/BRAF/PIK3CA wt metastatic CRC. Tumours with EGFR GCN below 4.0 appear to be as refractory to anti-EGFR treatment as tumours with mutation in any of the RAS/RAF/PIK3CA pathway genes.
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Affiliation(s)
- Annika Ålgars
- Department of Oncology, Turku University Hospital, Hämeentie 11, Turku, 20521, Finland.,MediCity Research Laboratory, University of Turku, Tykistökatu 6 A, Turku, 20520, Finland
| | - Jari Sundström
- Department of Pathology, University of Turku, Kiinamyllynkatu 10, Turku, 20520, Finland.,Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10, Turku, 20520, Finland
| | - Minnamaija Lintunen
- Department of Pathology, University of Turku, Kiinamyllynkatu 10, Turku, 20520, Finland.,Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10, Turku, 20520, Finland
| | - Terhi Jokilehto
- MediCity Research Laboratory, University of Turku, Tykistökatu 6 A, Turku, 20520, Finland.,Department of Pathology, University of Turku, Kiinamyllynkatu 10, Turku, 20520, Finland.,Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10, Turku, 20520, Finland
| | - Soili Kytölä
- HUSLAB, Division of Pathology and Genetics, Helsinki University Hospital, Topeliuksenkatu 32, Helsinki, 00029 HUS, Finland
| | - Milja Kaare
- HUSLAB, Division of Pathology and Genetics, Helsinki University Hospital, Topeliuksenkatu 32, Helsinki, 00029 HUS, Finland
| | - Reetta Vainionpää
- HUSLAB, Division of Pathology and Genetics, Helsinki University Hospital, Topeliuksenkatu 32, Helsinki, 00029 HUS, Finland
| | - Arto Orpana
- HUSLAB, Division of Pathology and Genetics, Helsinki University Hospital, Topeliuksenkatu 32, Helsinki, 00029 HUS, Finland
| | - Pia Österlund
- Department of Oncology, Helsinki University Hospital, Haartmaninkatu 4, P.O. Box 180, Helsinki, 00290, Finland.,Clinicum/Oncology, University of Helsinki, Haartmaninkatu 8, P.O. Box 63, Helsinki, 00014, Finland
| | - Ari Ristimäki
- Pathology, Research Programs Unit and HUSLAB, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, P.O. Box 21, Helsinki, 00014, Finland
| | - Olli Carpen
- Department of Pathology, University of Turku, Kiinamyllynkatu 10, Turku, 20520, Finland.,Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10, Turku, 20520, Finland.,Pathology, Research Programs Unit and HUSLAB, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, P.O. Box 21, Helsinki, 00014, Finland.,Auria Biobank, University of Turku and Turku University Hospital, Kiinamyllynkatu 8, Turku, 20521, Finland
| | - Raija Ristamäki
- Department of Oncology, Turku University Hospital, Hämeentie 11, Turku, 20521, Finland
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31
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Meehan K, Clynick B, Mirzai B, Maslen P, Harvey JM, Erber WN. HER2 mRNA transcript quantitation in breast cancer. Clin Transl Oncol 2016; 19:606-615. [PMID: 27837339 DOI: 10.1007/s12094-016-1573-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/31/2016] [Indexed: 12/15/2022]
Abstract
PURPOSE The human epidermal growth factor receptor 2 (HER2) status in breast cancer is important for prognostic prediction and the determination of optimal treatment. Current methods rely on protein expression, as determined by immunohistochemistry (IHC), as well as gene amplification as determined by in situ hybridisation (ISH). We explored whether quantitative droplet digital PCR (ddPCR) can be used for the detection and absolute quantitation of HER2 mRNA. METHODS Digital droplet PCR (ddPCR) was performed for HER2 mRNA on 178 formalin-fixed paraffin-embedded (FFPE) breast cancer specimens. HER2 positive, equivocal and negative cases as defined by standard criteria were included and both core biopsies and tissue sections were assessed. RESULTS HER2 positive cases contained significantly higher levels of HER2 mRNA (169-1,000,000 copies/µl) by ddPCR compared with equivocal (112-139 copies/µl, p = 0.025) and negative cases (6.2-644 copies/µl. p < 0.001). A continuum of transcript quantity was observed but a cutoff of 490 copies/µl distinguished between HER2 positive and negative cases. Results were consistent between core biopsy and tissue sections. CONCLUSIONS ddPCR can be used to quantify HER2 mRNA transcripts in FFPE breast cancer specimens. Our results highlight the potential of ddPCR on FFPE tissue to be used to accurately quantify HER2 transcripts. Validation in large cohorts will be required to determine a clinically applicable cutoff.
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Affiliation(s)
- K Meehan
- School of Pathology and Laboratory Medicine (M504), University of Western Australia, Crawley, WA, 6009, Australia.
| | - B Clynick
- School of Pathology and Laboratory Medicine (M504), University of Western Australia, Crawley, WA, 6009, Australia
| | - B Mirzai
- School of Pathology and Laboratory Medicine (M504), University of Western Australia, Crawley, WA, 6009, Australia
- PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, WA, 6009, Australia
| | - P Maslen
- School of Pathology and Laboratory Medicine (M504), University of Western Australia, Crawley, WA, 6009, Australia
| | - J M Harvey
- School of Pathology and Laboratory Medicine (M504), University of Western Australia, Crawley, WA, 6009, Australia
- PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, WA, 6009, Australia
| | - W N Erber
- School of Pathology and Laboratory Medicine (M504), University of Western Australia, Crawley, WA, 6009, Australia
- PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, WA, 6009, Australia
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Ahrberg CD, Manz A, Chung BG. Polymerase chain reaction in microfluidic devices. LAB ON A CHIP 2016; 16:3866-3884. [PMID: 27713993 DOI: 10.1039/c6lc00984k] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.
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Affiliation(s)
| | - Andreas Manz
- Microfluidics group, KIST-Europe, Saarbrücken, Germany and Mechanotronics Department, Universität des Saarlandes, Saarbrücken, Germany
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
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