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Corné J, Quillien V, Godey F, Cherel M, Cochet A, Le Du F, Robert L, Bourien H, Brunot A, Crouzet L, Perrin C, Lefeuvre-Plesse C, Diéras V, De la Motte Rouge T. Plasma-based analysis of ERBB2 mutational status by multiplex digital PCR in a large series of patients with metastatic breast cancer. Mol Oncol 2024. [PMID: 38287892 DOI: 10.1002/1878-0261.13592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/16/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
Erb-b2 receptor tyrosine kinase 2 (ERBB2)-activating mutations are therapeutically actionable alterations found in various cancers, including metastatic breast cancer (MBC). We developed multiplex digital PCR assays to detect and quantify ERBB2 mutations in circulating tumor DNA from liquid biopsies. We studied the plasma from 272 patients with hormone-receptor-positive, human epidermal growth factor receptor 2-negative (HR+/HER2-) MBC to detect 17 ERBB2 mutations using a screening assay. The assay was developed on the three-color Crystal dPCR™ naica® platform with a two-step strategy for precise mutation identification. We found that nine patients (3.3%) harbored at least one ERBB2 mutation. The mutation rate was higher in patients with lobular histology (5.9%) compared to invasive breast carcinoma of no special type (2.6%). A total of 12 mutations were found with the following frequencies: L755S (25.00%), V777L (25.00%), S310Y (16.67%), L869R (16.67%), S310F (8.33%), and D769H (8.33%). Matched tumor samples from six patients identified the same mutations with an 83% concordance rate. In summary, our highly sensitive multiplex digital PCR assays are well suited for plasma-based monitoring of ERBB2 mutational status in patients with MBC.
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Affiliation(s)
- Julien Corné
- Department of Biology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Véronique Quillien
- Department of Biology, Centre Eugène Marquis, Unicancer, Rennes, France
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
- INSERM U1242, University of Rennes, France
| | - Florence Godey
- Department of Biology, Centre Eugène Marquis, Unicancer, Rennes, France
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
- INSERM U1242, University of Rennes, France
| | - Mathilde Cherel
- Department of Biology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Agathe Cochet
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Fanny Le Du
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Lucie Robert
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Héloïse Bourien
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Angélique Brunot
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Laurence Crouzet
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Christophe Perrin
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | | | - Véronique Diéras
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
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Corné J, Quillien V, Callens C, Portois P, Bidard FC, Jeannot E, Godey F, Le Du F, Robert L, Bourien H, Brunot A, Crouzet L, Perrin C, Lefeuvre-Plesse C, Diéras V, De la Motte Rouge T. Development of sensitive and robust multiplex digital PCR assays for the detection of ESR1 mutations in the plasma of metastatic breast cancer patients. Clin Chim Acta 2023; 545:117366. [PMID: 37105452 DOI: 10.1016/j.cca.2023.117366] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]
Abstract
BACKGROUND Early detection of ESR1 mutations is a key element for better personalization of the management of patients with HR+/HER2- Metastatic Breast Cancer (MBC). Analysis of circulating tumor DNA from liquid biopsies is a particularly well-suited strategy for longitudinal monitoring of such patients. MATERIALS AND METHODS Using the naica® three-color digital PCR platform, we developed a screening assay allowing the detection of 11 ESR1 mutations and designed a sequential strategy for precise mutation identification. We then applied this strategy in the analysis of plasma circulating cell-free DNA from 109 HR+/HER2- MBC patients and performed a double-blind comparison study on a subset of patients, with the multiplex assay used at the Institut Curie (IC) for the PADA-1 study. RESULTS Thirty-one patients (28.4%) harboured at least one ESR1 mutation, with the following frequencies: D538G (41.03%), Y537S (25.64%), E380Q (10.26%), Y537N (10.26%), "(536-540)" (7.69%), Y537C (2.56%), and L536R (2.56%). The presence of ESR1 mutation(s) was significantly associated with liver metastases (p = 0.0091). A very good agreement (91%) was observed with the IC assay. CONCLUSION Our assays have proven to be robust and highly sensitive and are very well-suited for monitoring ESR1 mutations in the plasma of MBC patients.
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Affiliation(s)
- Julien Corné
- Department of Biology, Centre Eugène Marquis, Unicancer, Rennes, France.
| | - Véronique Quillien
- Department of Biology, Centre Eugène Marquis, Unicancer, Rennes, France; Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France; INSERM U1242, University of Rennes, Rennes, France
| | - Céline Callens
- Department of Genetics, Institut Curie, Paris and Saint-Cloud, France
| | - Pascal Portois
- Department of Genetics, Institut Curie, Paris and Saint-Cloud, France
| | | | - Emmanuelle Jeannot
- Department of Genetics, Institut Curie, Paris and Saint-Cloud, France; Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France; Department of Pathology, Institut Curie, Paris and Saint-Cloud, France
| | - Florence Godey
- Department of Biology, Centre Eugène Marquis, Unicancer, Rennes, France; Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France; INSERM U1242, University of Rennes, Rennes, France
| | - Fanny Le Du
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Lucie Robert
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Héloïse Bourien
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Angélique Brunot
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Laurence Crouzet
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Christophe Perrin
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | | | - Véronique Diéras
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
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Hu Q, Kanwal F, Lyu W, Zhang J, Liu X, Qin K, Shen F. Multiplex Digital Polymerase Chain Reaction on a Droplet Array SlipChip for Analysis of KRAS Mutations in Pancreatic Cancer. ACS Sens 2023; 8:114-121. [PMID: 36520653 DOI: 10.1021/acssensors.2c01776] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pancreatic cancer is a terminal disease with high mortality and very poor prognosis. A sensitive and quantitative analysis of KRAS mutations in pancreatic cancer provides a tool not only to understand the biological mechanisms of pancreatic cancer but also for diagnosis and treatment monitoring. Digital polymerase chain reaction (PCR) is a promising tool for KRAS mutation analysis, but current methods generally require a complex microfluidic handling system, which can be challenging to implement in routine research and point-of-care clinical diagnostics. Here, we present a droplet-array SlipChip (da-SlipChip) for the multiplex quantification of KRAS G12D, V, R, and C mutant genes with the wild-type (WT) gene background by dual color (FAM/ROX) fluorescence detection. This da-SlipChip is a high-density microwell array of 21,696 wells of 200 pL in 4 by 5424 microwell format with simple loading and slipping operation. It does not require the same precise alignment of microfeatures on the different plates that are acquired by the traditional digital PCR SlipChip. This device can provide accurate quantification of both mutant genes and the WT KRAS gene. We collected tumor tissue, paired normal pancreatic tissue, and other normal tissues from 18 pancreatic cancer patients and analyzed the mutation profiles of KRAS G12D, V, R, and C in these samples; the results from the multiplex digital PCR on da-SlipChip agree well with those of next-generation sequencing (NGS). This da-SlipChip moves digital PCR closer to the practical point-of-care applications not only for detecting KRAS mutations in pancreatic cancer but also for other applications that require precise nucleic acid quantification with high sensitivity.
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Affiliation(s)
- Qixin Hu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Fariha Kanwal
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Weiyuan Lyu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Jiajie Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Xu Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Kai Qin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
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Du M, Huang CC, Tan W, Kohli M, Wang L. Multiplex Digital PCR to Detect Amplifications of Specific Androgen Receptor Loci in Cell-Free DNA for Prognosis of Metastatic Castration-Resistant Prostate Cancer. Cancers (Basel) 2020; 12:E2139. [PMID: 32752286 PMCID: PMC7465398 DOI: 10.3390/cancers12082139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 11/16/2022] Open
Abstract
Amplification of androgen receptor (AR) is a common genomic event in metastatic castration-resistant prostate cancer (mCRPC). To evaluate the prognostic value of the amplifications of specific loci in the AR gene in cell-free DNA, we developed a multiplex digital PCR (dPCR) assay that targeted AR enhancer (AR-En), AR exon 1 (AR-E1), AR exon 8 (AR-E8) and OPHN1 (downstream of AR). We selected three relatively stable genes, C2orf16, FAM111B, and GRIA3, as reference controls for copy number normalization. One hundred and eight mCRPC patients were recruited to test the association of specific AR loci amplification with clinical outcome. Using a normalized ratio ≥ 1.92 as cutoff, amplification of AR-En, AR-E1, AR-E8 and OPHN1 was observed in 28, 25, 24 and 19 of 108 mCRPC patients, respectively. Among the 41 patients with AR region amplification, 9 (21.9%) showed amplification at all four selected regions and 15 (36.6%) showed amplification at AR-En, AR-E1, and AR-E8. Six (14.6%) patients showed independent AR-En amplification, while the remaining 3 (7.3%) demonstrated AR-E8 amplification only. Kaplan-Meier analysis showed overall survival's association with the amplification of AR-En (p = 0.02, HR = 1.68 (1.07-2.65)), AR-E8 (p = 0.02, HR = 1.78 (1.08-2.92)) and AR-En-E8 (the combination of AR-En and AR-E8 (p = 0.009, HR = 1.77 (1.15-2.73)). Multivariate models that included AR-En-E8 amplification and clinical factors significantly improved prognostic performance (p = 0.0001). With further validation, the multiplex dPCR assay may assist in prognostication of mCRPC patients.
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Affiliation(s)
- Meijun Du
- Department of the Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA;
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chiang-Ching Huang
- Department of Biostatistics, Zilber School of Public Health, University of Wisconsin, Milwaukee, WI 53205, USA;
| | - Winston Tan
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Jacksonville, FL 32224, USA;
| | - Manish Kohli
- Division of Oncology, Department of Medicine, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Liang Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
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