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Grolleau E, Candiracci J, Lescuyer G, Barthelemy D, Benzerdjeb N, Haon C, Geiguer F, Raffin M, Hardat N, Balandier J, Rabeuf R, Chalabreysse L, Wozny AS, Rommelaere G, Rodriguez-Lafrasse C, Subtil F, Couraud S, Herzog M, Payen-Gay L. Circulating H3K27 Methylated Nucleosome Plasma Concentration: Synergistic Information with Circulating Tumor DNA Molecular Profiling. Biomolecules 2023; 13:1255. [PMID: 37627320 PMCID: PMC10452235 DOI: 10.3390/biom13081255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The molecular profiling of circulating tumor DNA (ctDNA) is a helpful tool not only in cancer treatment, but also in the early detection of relapse. However, the clinical interpretation of a ctDNA negative result remains challenging. The characterization of circulating nucleosomes (carrying cell-free DNA) and associated epigenetic modifications (playing a key role in the tumorigenesis of different cancers) may provide useful information for patient management, by supporting the contributive value of ctDNA molecular profiling. Significantly elevated concentrations of H3K27Me3 nucleosomes were found in plasmas at the diagnosis, and during the follow-up, of NSCLC patients, compared to healthy donors (p-value < 0.0001). By combining the H3K27Me3 level and the ctDNA molecular profile, we found that 25.5% of the patients had H3K27Me3 levels above the cut off, and no somatic alteration was detected at diagnosis. This strongly supports the presence of non-mutated ctDNA in the corresponding plasma. During the patient follow-up, a high H3K27Me3-nucleosome level was found in 15.1% of the sample, despite no somatic mutations being detected, allowing the identification of disease progression from 43.1% to 58.2% over molecular profiling alone. Measuring H3K27Me3-nucleosome levels in combination with ctDNA molecular profiling may improve confidence in the negative molecular result for cfDNA in lung cancer at diagnosis, and may also be a promising biomarker for molecular residual disease (MRD) monitoring, during and/or after treatment.
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Affiliation(s)
- Emmanuel Grolleau
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Pulmonology Department, Lyon Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
| | - Julie Candiracci
- Belgian Volition SRL, Parc Scientifique Créalys, 5032 Isnes, Belgium
| | - Gaelle Lescuyer
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - David Barthelemy
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - Nazim Benzerdjeb
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Pathology Department, Claude Bernard University Lyon I, Hospices Civils de Lyon, 69677 Bron, France
| | - Christine Haon
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - Florence Geiguer
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - Margaux Raffin
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - Nathalie Hardat
- Belgian Volition SRL, Parc Scientifique Créalys, 5032 Isnes, Belgium
| | - Julie Balandier
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - Rémi Rabeuf
- Belgian Volition SRL, Parc Scientifique Créalys, 5032 Isnes, Belgium
| | - Lara Chalabreysse
- Pathology Department, Claude Bernard University Lyon I, Hospices Civils de Lyon, 69677 Bron, France
| | - Anne-Sophie Wozny
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
- Cellular and Molecular Radiobiology Laboratory UMR CNRS5822/IP2I, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
| | | | - Claire Rodriguez-Lafrasse
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
- Cellular and Molecular Radiobiology Laboratory UMR CNRS5822/IP2I, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
| | - Fabien Subtil
- Statistic Department, Hospices Civils de Lyon, 69008 Lyon, France
- LBBE, Claude Bernard University Lyon I, UMR 5558, CNRS, 69100 Villeurbanne, France
| | - Sébastien Couraud
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Pulmonology Department, Lyon Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
| | - Marielle Herzog
- Belgian Volition SRL, Parc Scientifique Créalys, 5032 Isnes, Belgium
| | - Lea Payen-Gay
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
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Bieler J, Kubik S, Macheret M, Pozzorini C, Willig A, Xu Z. Benefits of applying molecular barcoding systems are not uniform across different genomic applications. J Transl Med 2023; 21:305. [PMID: 37147717 PMCID: PMC10163729 DOI: 10.1186/s12967-023-04160-0] [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: 02/08/2023] [Accepted: 04/25/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Despite the wide variety of Next Generation Sequencing (NGS)-based methods, it remains challenging to detect mutations present at very low frequencies. This problem is particularly relevant in oncology, where the limiting amount of input material, and its low quality, often limit the performance of the assays. Unique Molecular Identifiers (UMIs) are a molecular barcoding system often coupled with computational methods of noise suppression to improve the reliability of detection of rare variants. Although widely adopted, UMI inclusion imposes additional technical complexity and sequencing cost. Currently, there are no guidelines on UMI usage nor a comprehensive evaluation of their advantage across different applications. METHODS We used DNA sequencing data generated by molecular barcoding and hybridization-based enrichment, from various types and quantities of input material (fresh frozen, formaldehyde-treated and cell-free DNA), to evaluate the performance of variant calling in different clinically relevant contexts. RESULTS Noise suppression achieved by read grouping based on fragment mapping positions ensures reliable variant calling for many experimental designs even without exogenous UMIs. Exogenous barcodes significantly improve performance only when mapping position collisions occur, which is common in cell-free DNA. CONCLUSIONS We demonstrate that UMI usage is not universally beneficial across experimental designs and that it is worthwhile to critically consider the comparative advantage of UMI usage for a given NGS application prior to experimental design.
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Affiliation(s)
- Jonathan Bieler
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland
| | - Slawomir Kubik
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland
| | - Morgane Macheret
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland
| | - Christian Pozzorini
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland
| | - Adrian Willig
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland
| | - Zhenyu Xu
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland.
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Paired Comparison of Routine Molecular Screening of Patient Samples with Advanced Non-Small Cell Lung Cancer in Circulating Cell-Free DNA Using Three Targeted Assays. Cancers (Basel) 2023; 15:cancers15051574. [PMID: 36900363 PMCID: PMC10001056 DOI: 10.3390/cancers15051574] [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: 12/30/2022] [Revised: 01/29/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
INTRODUCTION Progressive advanced non-small cell lung cancer (NSCLC) accounts for about 80-85% of all lung cancers. Approximately 10-50% of patients with NSCLC harbor targetable activating mutations, such as in-frame deletions in Exon 19 (Ex19del) of EGFR. Currently, for patients with advanced NSCLC, testing for sensitizing mutations in EGFR is mandatory prior to the administration of tyrosine kinase inhibitors. PATIENTS AND METHODS Plasma was collected from patients with NSCLC. We carried out targeted NGS using the Plasma-SeqSensei™ SOLID CANCER IVD kit on cfDNA (circulating free DNA). Clinical concordance for plasma detection of known oncogenic drivers was reported. In a subset of cases, validation was carried out using an orthogonal OncoBEAMTM EGFR V2 assay, as well as with our custom validated NGS assay. Somatic alterations were filtered, removing somatic mutations attributable to clonal hematopoiesis for our custom validated NGS assay. RESULTS In the plasma samples, driver targetable mutations were studied, with a mutant allele frequency (MAF) ranging from 0.00% (negative detection) to 82.25%, using the targeted next-generation sequencing Plasma-SeqSensei™ SOLID CANCER IVD Kit. In comparison with the OncoBEAMTM EGFR V2 kit, the EGFR concordance is 89.16% (based on the common genomic regions). The sensitivity and specificity rates based on the genomic regions (EGFR exons 18, 19, 20, and 21) were 84.62% and 94.67%. Furthermore, the observed clinical genomic discordances were present in 25% of the samples: 5% in those linked to the lower of coverage of the OncoBEAMTM EGFR V2 kit, 7% in those induced by the sensitivity limit on the EGFR with the Plasma-SeqSensei™ SOLID CANCER IVD Kit, and 13% in the samples linked to the larger KRAS, PIK3CA, BRAF coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit. Most of these somatic alterations were cross validated in our orthogonal custom validated NGS assay, used in the routine management of patients. The concordance is 82.19% in the common genomic regions (EGFR exons 18, 19, 20, 21; KRAS exons 2, 3, 4; BRAF exons 11, 15; and PIK3CA exons 10, 21). The sensitivity and specificity rates were 89.38% and 76.12%, respectively. The 32% of genomic discordances were composed of 5% caused by the limit of coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit, 11% induced by the sensitivity limit of our custom validated NGS assay, and 16% linked to the additional oncodriver analysis, which is only covered by our custom validated NGS assay. CONCLUSIONS The Plasma-SeqSensei™ SOLID CANCER IVD kit resulted in de novo detection of targetable oncogenic drivers and resistance alterations, with a high sensitivity and accuracy for low and high cfDNA inputs. Thus, this assay is a sensitive, robust, and accurate test.
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Rousset X, Maillet D, Grolleau E, Barthelemy D, Calattini S, Brevet M, Balandier J, Raffin M, Geiguer F, Garcia J, Decaussin-Petrucci M, Peron J, Benzerdjeb N, Couraud S, Viallet J, Payen L. Embryonated Chicken Tumor Xenografts Derived from Circulating Tumor Cells as a Relevant Model to Study Metastatic Dissemination: A Proof of Concept. Cancers (Basel) 2022; 14:cancers14174085. [PMID: 36077622 PMCID: PMC9454737 DOI: 10.3390/cancers14174085] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/21/2022] [Accepted: 08/19/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Circulating Tumor Cells (CTCs) are heterogeneous and rare in the bloodstream, but responsible for cancer metastasis. Their in vitro or in vivo expansion remains a major challenge. The chicken Chorioallantoic Membrane (CAM) assay has proven to be a reliable alternative to the murine model, notably for tumor xenografts. We have developed a promising model of CTC-derived xenografts in the chicken CAM and demonstrated the feasibility of Next Generation Sequencing (NGS) analysis in this assay, with a genomic concordance between the in ovo tumor and the original patient’s tumor. We also evidenced metastatic dissemination from the xenograft in the chicken embryo’s distant organs. Further characterization of the in ovo tumors and metastases may provide new insights into the mechanisms of tumor dissemination. The development of a xenograft from a given patient’s CTCs, in a time frame compatible with managing the patient’s treatment, could also be a step forward towards personalized medicine. Abstract Patient-Derived Xenografts (PDXs) in the Chorioallantoic Membrane (CAM) are a representative model for studying human tumors. Circulating Tumor Cells (CTCs) are involved in cancer dissemination and treatment resistance mechanisms. To facilitate research and deep analysis of these few cells, significant efforts were made to expand them. We evaluated here whether the isolation of fresh CTCs from patients with metastatic cancers could provide a reliable tumor model after a CAM xenograft. We enrolled 35 patients, with breast, prostate, or lung metastatic cancers. We performed microfluidic-based CTC enrichment. After 48–72 h of culture, the CTCs were engrafted onto the CAM of embryonated chicken eggs at day 9 of embryonic development (EDD9). The tumors were resected 9 days after engraftment and histopathological, immunochemical, and genomic analyses were performed. We obtained in ovo tumors for 61% of the patients. Dedifferentiated small tumors with spindle-shaped cells were observed. The epithelial-to-mesenchymal transition of CTCs could explain this phenotype. Beyond the feasibility of NGS in this model, we have highlighted a genomic concordance between the in ovo tumor and the original patient’s tumor for constitutional polymorphism and somatic alteration in one patient. Alu DNA sequences were detected in the chicken embryo’s distant organs, supporting the idea of dedifferentiated cells with aggressive behavior. To our knowledge, we performed the first chicken CAM CTC-derived xenografts with NGS analysis and evidence of CTC dissemination in the chicken embryo.
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Affiliation(s)
| | - Denis Maillet
- University Claude Bernard Lyon, 69100 Villeurbanne, France
- Department of Medical Oncology, Lyon Sud Hospital, Hospices Civils de Lyon, 69310 Pierre-Bénite, France
- Centre de Recherche en Cancérologie de Lyon, INSERM 1052 CNRS UMR 5286, 69008 Lyon, France
| | - Emmanuel Grolleau
- University Claude Bernard Lyon, 69100 Villeurbanne, France
- Acute Respiratory Disease and Thoracic Oncology Department, Lyon Sud Hospital, Hospices Civils de Lyon, 69310 Pierre-Bénite, France
- EMR-3738 Therapeutic Targeting in Oncology, Lyon Sud Medical Faculty, 69000 Lyon, France
| | - David Barthelemy
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre Bénite, France
| | - Sara Calattini
- Clinical Research Plateform, Institut de Cancérologie des Hospices Civils de Lyon, 69002 Lyon, France
| | - Marie Brevet
- Department of Pathology, Lyon Est Hospital, Hospices Civils de Lyon, 69677 Bron, France
| | - Julie Balandier
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre Bénite, France
| | - Margaux Raffin
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre Bénite, France
| | - Florence Geiguer
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre Bénite, France
| | - Jessica Garcia
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre Bénite, France
| | - Myriam Decaussin-Petrucci
- University Claude Bernard Lyon, 69100 Villeurbanne, France
- EMR-3738 Therapeutic Targeting in Oncology, Lyon Sud Medical Faculty, 69000 Lyon, France
- Department of Pathology, Lyon Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
| | - Julien Peron
- University Claude Bernard Lyon, 69100 Villeurbanne, France
- Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, CNRS UMR 5558, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
| | - Nazim Benzerdjeb
- University Claude Bernard Lyon, 69100 Villeurbanne, France
- EMR-3738 Therapeutic Targeting in Oncology, Lyon Sud Medical Faculty, 69000 Lyon, France
- Department of Pathology, Lyon Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
| | - Sébastien Couraud
- University Claude Bernard Lyon, 69100 Villeurbanne, France
- Acute Respiratory Disease and Thoracic Oncology Department, Lyon Sud Hospital, Hospices Civils de Lyon, 69310 Pierre-Bénite, France
- EMR-3738 Therapeutic Targeting in Oncology, Lyon Sud Medical Faculty, 69000 Lyon, France
| | | | - Léa Payen
- University Claude Bernard Lyon, 69100 Villeurbanne, France
- EMR-3738 Therapeutic Targeting in Oncology, Lyon Sud Medical Faculty, 69000 Lyon, France
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre Bénite, France
- Correspondence:
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