Frontiers in Oncology (May 2021)
Characterization of Plasma Cell-Free DNA Integrity Using Droplet-Based Digital PCR: Toward the Development of Circulating Tumor DNA-Dedicated Assays
- Geoffroy Poulet,
- Geoffroy Poulet,
- Fanny Garlan,
- Sonia Garrigou,
- Eleonora Zonta,
- Leonor Benhaim,
- Leonor Benhaim,
- Marie-Jennifer Carrillon,
- Audrey Didelot,
- Delphine Le Corre,
- Claire Mulot,
- Claire Mulot,
- Philippe Nizard,
- Frederic Ginot,
- Audrey Boutonnet-Rodat,
- Helene Blons,
- Helene Blons,
- Jean-Baptiste Bachet,
- Jean-Baptiste Bachet,
- Jean-Baptiste Bachet,
- Jean-Baptiste Bachet,
- Julien Taïeb,
- Julien Taïeb,
- Julien Taïeb,
- Aziz Zaanan,
- Aziz Zaanan,
- Vanna Geromel,
- Laurence Pellegrina,
- Pierre Laurent-Puig,
- Pierre Laurent-Puig,
- Shu-Fang Wang-Renault,
- Valerie Taly
Affiliations
- Geoffroy Poulet
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Geoffroy Poulet
- Eurofins-Biomnis, Specialized Medical Biology Laboratory, Lyon, France
- Fanny Garlan
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Sonia Garrigou
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Eleonora Zonta
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Leonor Benhaim
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Leonor Benhaim
- Department of Visceral and Surgical Oncology, Gustave Roussy, Villejuif, France
- Marie-Jennifer Carrillon
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Audrey Didelot
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Delphine Le Corre
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Claire Mulot
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Claire Mulot
- CIC-EC4 URC, HEGP, Hôpitaux Universitaires Paris Ouest AP-HP, Paris, France
- Philippe Nizard
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Frederic Ginot
- Adelis, ID-solutions, Labège, France
- Audrey Boutonnet-Rodat
- Adelis, ID-solutions, Labège, France
- Helene Blons
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Helene Blons
- Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France
- Jean-Baptiste Bachet
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Jean-Baptiste Bachet
- Sorbonne Universités, UPMC Université, Paris, France
- Jean-Baptiste Bachet
- Department of Hepato-gastroenterology, Groupe Hospitalier Pitié Salpêtrière, Paris, France
- Jean-Baptiste Bachet
- AGEO (Association des Gastroentérologues Oncologues), Paris, France
- Julien Taïeb
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Julien Taïeb
- Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France
- Julien Taïeb
- AGEO (Association des Gastroentérologues Oncologues), Paris, France
- Aziz Zaanan
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Aziz Zaanan
- Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France
- Vanna Geromel
- Eurofins-Biomnis, Specialized Medical Biology Laboratory, Lyon, France
- Laurence Pellegrina
- Eurofins-Biomnis, Specialized Medical Biology Laboratory, Lyon, France
- Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Pierre Laurent-Puig
- Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France
- Shu-Fang Wang-Renault
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- Valerie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
- DOI
- https://doi.org/10.3389/fonc.2021.639675
- Journal volume & issue
-
Vol. 11
Abstract
Background: Cellular-cell free-DNA (ccfDNA) is being explored as a diagnostic and prognostic tool for various diseases including cancer. Beyond the evaluation of the ccfDNA mutational status, its fragmentation has been investigated as a potential cancer biomarker in several studies. However, probably due to a lack of standardized procedures dedicated to preanalytical and analytical processing of plasma samples, contradictory results have been published.Methods: ddPCR assays allowing the detection of KRAS wild-type and mutated sequences (KRAS p.G12V, pG12D, and pG13D) were designed to target different fragments sizes. Once validated on fragmented and non-fragmented DNA extracted from cancer cell lines, these assays were used to investigate the influence of the extraction methods on the non-mutated and mutated ccfDNA integrity reflected by the DNA integrity index (DII). The DII was then analyzed in two prospective cohorts of metastatic colorectal cancer patients (RASANC study n = 34; PLACOL study n = 12) and healthy subjects (n = 49).Results and Discussion: Our results demonstrate that ccfDNA is highly fragmented in mCRC patients compared with healthy individuals. These results strongly suggest that the characterization of ccfDNA integrity hold great promise toward the development of a universal biomarker for the follow-up of mCRC patients. Furthermore, they support the importance of standardization of sample handling and processing in such analysis.
Keywords
- circulating tumor DNA
- picoliter-droplet digital PCR
- cancer biomarker
- apoptosis
- necrosis
- DNA integrity index
