Audrey Didelot
Paris Descartes University
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Featured researches published by Audrey Didelot.
Clinical Chemistry | 2013
Audrey Didelot; Steve Kotsopoulos; Audrey Lupo; Deniz Pekin; Xinyu Li; Ivan Atochin; Preethi Srinivasan; Qun Zhong; Jeffrey J. Olson; Darren R. Link; Pierre Laurent-Puig; Hélène Blons; J. Brian Hutchison; Valérie Taly
BACKGROUND Assessment of DNA integrity and quantity remains a bottleneck for high-throughput molecular genotyping technologies, including next-generation sequencing. In particular, DNA extracted from paraffin-embedded tissues, a major potential source of tumor DNA, varies widely in quality, leading to unpredictable sequencing data. We describe a picoliter droplet-based digital PCR method that enables simultaneous detection of DNA integrity and the quantity of amplifiable DNA. METHODS Using a multiplex assay, we detected 4 different target lengths (78, 159, 197, and 550 bp). Assays were validated with human genomic DNA fragmented to sizes of 170 bp to 3000 bp. The technique was validated with DNA quantities as low as 1 ng. We evaluated 12 DNA samples extracted from paraffin-embedded lung adenocarcinoma tissues. RESULTS One sample contained no amplifiable DNA. The fractions of amplifiable DNA for the 11 other samples were between 0.05% and 10.1% for 78-bp fragments and ≤1% for longer fragments. Four samples were chosen for enrichment and next-generation sequencing. The quality of the sequencing data was in agreement with the results of the DNA-integrity test. Specifically, DNA with low integrity yielded sequencing results with lower levels of coverage and uniformity and had higher levels of false-positive variants. CONCLUSIONS The development of DNA-quality assays will enable researchers to downselect samples or process more DNA to achieve reliable genome sequencing with the highest possible efficiency of cost and effort, as well as minimize the waste of precious samples.
Clinical Chemistry | 2016
Sonia Garrigou; Géraldine Perkins; Fanny Garlan; Corinne Normand; Audrey Didelot; Delphine Le Corre; Sanam Peyvandi; Claire Mulot; Ralph Niarra; Pascaline Aucouturier; Gilles Chatellier; Philippe Nizard; Karla Perez-Toralla; Eleonora Zonta; Cécile Charpy; Anais Pujals; Caroline Barau; Olivier Bouché; Jean-François Emile; Denis Pezet; Frédéric Bibeau; J. Brian Hutchison; Darren R. Link; Aziz Zaanan; Pierre Laurent-Puig; Iradj Sobhani; Valérie Taly
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a good candidate for tracking tumor dynamics in different cancer types, potentially avoiding repeated tumor biopsies. Many different genes can be mutated within a tumor, complicating procedures for tumor monitoring, even with highly sensitive next-generation sequencing (NGS) strategies. Droplet-based digital PCR (dPCR) is a highly sensitive and quantitative procedure, allowing detection of very low amounts of circulating tumor genetic material, but can be limited in the total number of target loci monitored. METHODS We analyzed hypermethylation of 3 genes, by use of droplet-based dPCR in different stages of colorectal cancer (CRC), to identify universal markers for tumor follow-up. RESULTS Hypermethylation of WIF1 (WNT inhibitory factor 1) and NPY (neuropeptide Y) genes was significantly higher in tumor tissue compared to normal tissue, independently of tumor stage. All tumor tissues appeared positive for one of the 2 markers. Methylated ctDNA (MetctDNA) was detected in 80% of metastatic CRC and 45% of localized CRC. For samples with detectable mutations in ctDNA, MetctDNA and mutant ctDNA (MutctDNA) fractions were correlated. During follow-up of different stage CRC patients, MetctDNA changes allowed monitoring of tumor evolution. CONCLUSIONS These results indicate that MetctDNA could be used as a universal surrogate marker for tumor follow-up in CRC patients, and monitoring MetctDNA by droplet-based dPCR could avoid the need for monitoring mutations.
Clinical Cancer Research | 2017
Daniel Pietrasz; Nicolas Pécuchet; Fanny Garlan; Audrey Didelot; Olivier Dubreuil; Solène Doat; Francoise Imbert-Bismut; Mehdi Karoui; Jean-Christophe Vaillant; Valérie Taly; Pierre Laurent-Puig; Jean-Baptiste Bachet
Purpose: Despite recent therapeutic advances, prognosis of patients with pancreatic adenocarcinoma remains poor. Analyses from tumor tissues present limitations; identification of informative marker from blood might be a promising alternative. The aim of this study was to assess the feasibility and the prognostic value of circulating tumor DNA (ctDNA) in pancreatic adenocarcinoma. Experimental Design: From 2011 to 2015, blood samples were prospectively collected from all consecutive patients with pancreatic adenocarcinoma treated in our center. Identification of ctDNA was done with next-generation sequencing targeted on referenced mutations in pancreatic adenocarcinoma and with picoliter droplet digital PCR. Results: A total of 135 patients with resectable (n = 31; 23%), locally advanced (n = 36; 27%), or metastatic (n = 68; 50%) pancreatic adenocarcinoma were included. In patients with advanced pancreatic adenocarcinoma (n = 104), 48% (n = 50) had ctDNA detectable with a median mutation allelic frequency (MAF) of 6.1%. The presence of ctDNA was strongly correlated with poor overall survival (OS; 6.5 vs. 19.0 months; P < 0.001) in univariate and multivariate analyses (HR = 1.96; P = 0.007). To evaluate the impact of ctDNA level, patients were grouped according to MAF tertiles: OS were 18.9, 7.8, and 4.9 months (P < 0.001). Among patients who had curative intent resection (n = 31), 6 had ctDNA detectable after surgery, with an MAF of 4.4%. The presence of ctDNA was associated with a shorter disease-free survival (4.6 vs.17.6 months; P = 0.03) and shorter OS (19.3 vs. 32.2 months; P = 0.027). Conclusions: ctDNA is an independent prognostic marker in advanced pancreatic adenocarcinoma. Furthermore, it arises as an indicator of shorter disease-free survival in resected patients when detected after surgery. Clin Cancer Res; 23(1); 116–23. ©2016 AACR.
PLOS Medicine | 2016
Nicolas Pécuchet; Eleonora Zonta; Audrey Didelot; Pierre Combe; Constance Thibault; Laure Gibault; Camille Lours; Yves Rozenholc; Valérie Taly; Pierre Laurent-Puig; Hélène Blons; Elizabeth Fabre
Background Circulating tumor DNA (ctDNA) is an approved noninvasive biomarker to test for the presence of EGFR mutations at diagnosis or recurrence of lung cancer. However, studies evaluating ctDNA as a noninvasive “real-time” biomarker to provide prognostic and predictive information in treatment monitoring have given inconsistent results, mainly due to methodological differences. We have recently validated a next-generation sequencing (NGS) approach to detect ctDNA. Using this new approach, we evaluated the clinical usefulness of ctDNA monitoring in a prospective observational series of patients with non-small cell lung cancer (NSCLC). Methods and Findings We recruited 124 patients with newly diagnosed advanced NSCLC for ctDNA monitoring. The primary objective was to analyze the prognostic value of baseline ctDNA on overall survival. ctDNA was assessed by ultra-deep targeted NGS using our dedicated variant caller algorithm. Common mutations were validated by digital PCR. Out of the 109 patients with at least one follow-up marker mutation, plasma samples were contributive at baseline (n = 105), at first evaluation (n = 85), and at tumor progression (n = 66). We found that the presence of ctDNA at baseline was an independent marker of poor prognosis, with a median overall survival of 13.6 versus 21.5 mo (adjusted hazard ratio [HR] 1.82, 95% CI 1.01–3.55, p = 0.045) and a median progression-free survival of 4.9 versus 10.4 mo (adjusted HR 2.14, 95% CI 1.30–3.67, p = 0.002). It was also related to the presence of bone and liver metastasis. At first evaluation (E1) after treatment initiation, residual ctDNA was an early predictor of treatment benefit as judged by best radiological response and progression-free survival. Finally, negative ctDNA at E1 was associated with overall survival independently of Response Evaluation Criteria in Solid Tumors (RECIST) (HR 3.27, 95% CI 1.66–6.40, p < 0.001). Study population heterogeneity, over-representation of EGFR-mutated patients, and heterogeneous treatment types might limit the conclusions of this study, which require future validation in independent populations. Conclusions In this study of patients with newly diagnosed NSCLC, we found that ctDNA detection using targeted NGS was associated with poor prognosis. The heterogeneity of lung cancer molecular alterations, particularly at time of progression, impairs the ability of individual gene testing to accurately detect ctDNA in unselected patients. Further investigations are needed to evaluate the clinical impact of earlier evaluation times at 1 or 2 wk. Supporting clinical decisions, such as early treatment switching based on ctDNA positivity at first evaluation, will require dedicated interventional studies.
Clinical Cancer Research | 2017
Fanny Garlan; Pierre Laurent-Puig; David Sefrioui; N. Siauve; Audrey Didelot; Nasrin Sarafan-Vasseur; Pierre Michel; Géraldine Perkins; Claire Mulot; Hélène Blons; Julien Taieb; Frédéric Di Fiore; Valérie Taly; Aziz Zaanan
Purpose: Markers of chemotherapy efficacy in metastatic colorectal cancer (mCRC) are essential for optimization of treatment strategies. We evaluated the applicability of early changes in circulating tumor DNA (ctDNA) as a marker of therapeutic efficacy. Experimental Design: This prospective study enrolled consecutive patients with mCRC receiving a first- or second-line chemotherapy. CtDNA was assessed in plasma collected before the first (C0), second (C1) and/or third (C2) chemotherapy cycle, using picodroplet-digital PCR assays based either on detection of gene mutation (KRAS, BRAF, TP53) or hypermethylation (WIF1, NPY). CT scans were centrally assessed using RECIST v1.1 criteria. Multivariate analyses were adjusted on age, gender, ECOG performance status (PS), metastatic synchronicity, and treatment line. Results: Eighty-two patients with mCRC treated in first- (82.9%) or second- (17.1%) line chemotherapy were included. Patients with a high (>10 ng/mL) versus low (≤0.1 ng/mL) ctDNA concentration at C0 had a shorter overall survival (OS; 6.8 vs. 33.4 months: adjusted HR, 5.64; 95% CI, 2.5–12.6; P < 0.0001). By analyzing the evolution of the ctDNA concentration between C0 and C2 or C1 (C2or1), we classified the patients in two groups (named “good” or “bad ctDNA responders”). In multivariate analysis, patients belonging to the group called “good ctDNA responder” (n = 58) versus “bad ctDNA responder” (n = 15) had a better objective response rate (P < 0.001), and a longer median progression-free survival (8.5 vs. 2.4 months: HR, 0.19; 95% CI, 0.09–0.40; P < 0.0001) and OS (27.1 vs. 11.2 months: HR, 0.25; 95% CI, 0.11–0.57; P < 0.001). Conclusions: This study suggests that early change in ctDNA concentration is a marker of therapeutic efficacy in patients with mCRC. Clin Cancer Res; 23(18); 5416–25. ©2017 AACR.
Oncotarget | 2017
Nicolas Pécuchet; Pierre Laurent-Puig; Audrey Mansuet-Lupo; Antoine Legras; Marco Alifano; Karine Pallier; Audrey Didelot; Laure Gibault; Claire Danel; Pierre-Alexandre Just; Marc Riquet; Françoise Le Pimpec-Barthes; Diane Damotte; E. Fabre; Hélène Blons
STK11 is commonly mutated in lung cancer. In light of recent experimental data showing that specific STK11 mutants could acquire oncogenic activities due to the synthesis of a short STK11 isoform, we investigated whether this new classification of STK11 mutants could help refine its role as a prognostic marker. We conducted a retrospective high-throughput genotyping study in 567 resected non-squamous non-small-cell lung cancer (NSCLC) patients. STK11 exons 1 or 2 mutations (STK11ex1-2) with potential oncogenic activity were analyzed separately from exons 3 to 9 (STK11ex3-9). STK11ex1-2 and STK11ex3-9 mutations occurred in 5% and 14% of NSCLC. STK11 mutated patients were younger (P = .01) and smokers (P< .0001). STK11 mutations were significantly associated with KRAS and inversely with EGFR mutations. After a median follow-up of 7.2 years (95%CI 6.8-.4), patients with STK11ex1-2 mutation had a median OS of 24 months (95%CI 15-57) as compared to 69 months (95%CI 56-93) for wild-type (log-rank, P = .005) and to 91 months (95%CI 57-unreached) for STK11ex3-9 mutations (P = .003). In multivariate analysis, STK11ex1-2 mutations remained associated with a poor prognosis (P = .002). Results were validated in two public datasets. Western blots showed that STK11ex1-2 mutatedtumors expressed short STK11 isoforms. Finally using mRNAseq data from the TCGA cohort, we showed that a stroma-derived poor prognosis signature was enriched in STK11ex1-2 mutated tumors. All together our results show that STK11ex1-2 mutations delineate an aggressive subtype of lung cancer for which a targeted treatment through STK11 inhibition might offer new opportunities.
Cancers | 2017
Antoine Legras; Nicolas Pécuchet; Sandrine Imbeaud; Karine Pallier; Audrey Didelot; Hélène Roussel; Laure Gibault; Elizabeth Fabre; Françoise Le Pimpec-Barthes; Pierre Laurent-Puig; Hélène Blons
Despite major advances, non-small cell lung cancer (NSCLC) remains the major cause of cancer-related death in developed countries. Metastasis and drug resistance are the main factors contributing to relapse and death. Epithelial-to-mesenchymal transition (EMT) is a complex molecular and cellular process involved in tissue remodelling that was extensively studied as an actor of tumour progression, metastasis and drug resistance in many cancer types and in lung cancers. Here we described with an emphasis on NSCLC how the changes in signalling pathways, transcription factors expression or microRNAs that occur in cancer promote EMT. Understanding the biology of EMT will help to define reversing process and treatment strategies. We will see that this complex mechanism is related to inflammation, cell mobility and stem cell features and that it is a dynamic process. The existence of intermediate phenotypes and tumour heterogeneity may be debated in the literature concerning EMT markers, EMT signatures and clinical consequences in NSCLC. However, given the role of EMT in metastasis and in drug resistance the development of EMT inhibitors is an interesting approach to counteract tumour progression and drug resistance. This review describes EMT involvement in cancer with an emphasis on NSCLC and microRNA regulation.
Analytical Chemistry | 2018
Comtet-Louis Andriamanampisoa; Aurélien Bancaud; Audrey Boutonnet-Rodat; Audrey Didelot; Jacques Fabre; F. Fina; Fanny Garlan; Sonia Garrigou; Caroline Gaudy; Frédéric Ginot; Daniel Henaff; Pierre Laurent-Puig; Arnaud Morin; Vincent Picot; Laure Saias; Valérie Taly; Pascale Tomasini; Aziz Zaanan
We describe a technology to perform sizing and concentration analysis of double stranded DNA with a sensitivity of 10 fg/μL in an operating time of 20 min. The technology is operated automatically on a commercial capillary electrophoresis instrument using electro-hydrodynamic actuation. It relies on a new capillary device that achieves online concentration of DNA at the junction between two capillaries of different diameters, thanks to viscoelastic lift forces. Using a set of DNA ladders in the range of 100-1500 bp, we report a sizing accuracy and precision better than 3% and a concentration quantification precision of ∼20%. When the technology is applied to the analysis of clinical samples of circulating cell-free DNA (cfDNA), the measured cfDNA concentrations are in good correlation with those measured by digital PCR. Furthermore, the cfDNA size profiles indicate that the fraction of low molecular weight cfDNA in the range of 75-240 bp is a candidate biomarker to discriminate between healthy subjects and cancer patients. We conclude that our technology is efficient in analyzing highly diluted DNA samples and suggest that it will be helpful in translational and clinical research involving cfDNA.
Journal of Thoracic Disease | 2018
Antoine Legras; Anne Tallet; Audrey Didelot; Aurélie Cazes; Claire Danel; Angela Hin; Raphael Borie; Bruno Crestani; Yves Castier; Patrick Bagan; Françoise Le Pimpec-Barthes; Marc Riquet; Hélène Blons; Pierre Mordant
Background Unicentric mediastinal Castleman disease (CD) is a rare condition, poorly characterized due to the small number of cases and the absence of genomic study. We analyzed clinical, radiological, histological and genomic patterns associated with mediastinal CD in a substantial case series.Methods: We retrospectively reviewed cases of unicentric mediastinal CD managed in 2 French thoracic surgery departments between 1988 and 2012. Clinical, radiological, surgical and pathological data were recorded. On available FFPE blocks we performed mutation screening by next-generation-sequencing, using AmpliSeq™ Cancer Hotspot v2 (Life Technologies) and immunohistochemistry (IHC) (AKT-mTOR pathway). Results Eleven patients were identified (mean age 41±15 years, sex-ratio 0.8, median follow-up 78 months). Surgical approach was thoracotomy (n=6), sternotomy (n=4), and VATS (n=1). Additional procedures included thymectomy in three cases, mediastinal lymphadenectomy in two cases, and bilobectomy in one case. One patient presented local relapse as a follicular dendritic cell sarcoma, leading to death 48 months after the first resection. Within 9 patients whose FFPE blocks were available, 2 mutations were found: VHL (p.F119L, 35%, n=1) and JAK3 (p.V718L, 53%, n=1). Phospho-AKT and phospho-mTOR stainings were negative in all cases, whereas phospho-S6RP staining was positive in eight cases, mainly in interfollicular cell cytoplasm. Conclusions From this series of patients with unicentric mediastinal CD, we observed 2 cases of potential driver mutations and 8 cases of phospho-S6RP activation not related to AKT-mTOR. Larger studies are required to decipher more precisely the molecular abnormalities and potential therapeutic targets underlying this uncommon condition.
Cancer Research | 2017
Jose L. Costa; Robbert D.A. Weren; Anna Maria Rachiglio; Andrea Mafficini; Henriette Kurth; Anne Reiman; Audrey Didelot; Alexander Boag; Claudia Vollbrecht; Kazuto Nishino; Harriet Feilotter; Pierre Laurent-Puig; Orla Sheils; Aldo Scarpa; Marjolijn J. L. Ligtenberg; Ian A. Cree; Michael Hummel; José Carlos Machado; Nicola Normanno
Introduction: The detection of actionable mutations in lung cancer is still a major challenge due to the lack of tissue specimens for molecular profiling of the tumor in approximately 25% of patients. The circulating cell-free tumor DNA (ctDNA) isolated from plasma of cancer patients is an alternative, minimally invasive source of tumor DNA that also allows rapid determination of the mutational status of the tumor. However, the intrinsic low abundance of mutations in cfDNA makes their detection and quantification in plasma a challenging task. Here we report a multi-institutional validation of the Oncomine cfDNA Lung Cancer assay for the analyses of cfDNA in molecular pathology laboratories. Methods: The Oncomine cfDNA Lung assays is a multiplexed sequencing assay for liquid biopsy that generates reads containing targeted ctDNA regions along with a molecular tag. In order to allow an initial uniform evaluation of the assay, the Multiplex I cfDNA Reference Standard (Horizon Dx) derived from human cell lines, and fragmented to an average size of 160bp±10% (144bp–176bp) to closely resemble cfDNA extracted from human plasma, was used. The reference sample covers 8 mutations in the EGFR, KRAS, NRAS and PIK3CA genes at 5%, 1%, 0.1% allelic frequencies and wildtype allele. The same lot of control sample was distributed to the participating laboratories within the OncoNetwork Consortium. Samples were sequenced twice in each laboratory either using the Ion PGM system or the Ion S5 system. Libraries were templated using the Ion Chef and multiplexed as four libraries on a 318/520 chip or eight libraries on a 530 chip. A bioinformatics pipeline within the Torrent Server software allowed for automated variant calling. Results: The laboratories involved in the study were able to detect the 8 hotspot base changes and indels present in the control samples at allelic frequencies from 0.1% to 5% with an average 94.05% sensitivity (range 87.50% - 97.92%) and an average 99.87% specificity (range 99.53% - 100%). When only considering variants at the 0.1% allelic frequency, the average sensitivity was 83.04% (range 68.75% - 99.95%) and the average specificity was 99.95% (range 99.68% - 99.95%). Notably, at the 0.1% allelic frequency, all the participating laboratories were able to detect the challenging EGFR p.T790M variant that is a marker of sensitivity to EGFR tyrosine kinase inhibitors. Conclusions: These preliminary data confirm the potential of the Oncomine cfDNA lung assay for plasma genotyping to allow for the noninvasive, multiplexed detection of complex, targetable genomic alterations in lung cancer. Citation Format: Jose L. Costa, Robbert Weren, Anna Maria Rachiglio, Andrea Mafficini, Henriette Kurth, Anne Reiman, Audrey Didelot, Alexander Boag, Claudia Vollbrecht, Kazuto Nishino, Harriet E. Feilotter, Pierre Laurent-Puig, Orla Sheils, Aldo Scarpa, Marjolijn Ligtenberg, Ian A. Cree, Michael Hummel, Jose Carlos Machado, Nicola Normanno. Multi institutional evaluation of a new NGS assay for mutation detection from cfDNA in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5694. doi:10.1158/1538-7445.AM2017-5694