Highly Specific Droplet-Digital PCR Detection of Universally Methylated Circulating Tumor DNA in Endometrial Carcinoma.

Biomarkers, Tumor / genetics Circulating Tumor DNA / genetics Endometrial Neoplasms / diagnosis Female Humans Polymerase Chain Reaction / methods Prospective Studies Retrospective Studies
DNA methylation digital droplet PCR endometrial carcinoma molecular characterization personalized medicine

Journal

Clinical chemistry
ISSN: 1530-8561
Titre abrégé: Clin Chem
Pays: England
ID NLM: 9421549

Informations de publication

Date de publication:
01 06 2022
Historique:
received: 24 10 2021
accepted: 07 01 2022
pubmed: 25 3 2022
medline: 3 6 2022
entrez: 24 3 2022
Statut: ppublish

Résumé

No circulating biomarker is available for endometrial carcinoma (EC). We aimed to identify DNA positions universally hypermethylated in EC, and to develop a digital droplet PCR (ddPCR) assay for detection of hypermethylated circulating tumor DNA (meth-ctDNA) in plasma from patients with EC. DNA positions hypermethylated in EC, and without unspecific hypermethylation in tissue/cell types releasing circulating cell-free DNA in plasma, were identified in silico from TCGA/Gene Expression Omnibus (GEO) data. A methylation-specific ddPCR (meth-ddPCR) assay following bisulfite conversion of DNA extracted from plasma was optimized for detection of meth-ctDNA according to dMIQE guidelines. Performances were validated on a retrospective cohort (n = 78 tumors, n = 30 tumor-adjacent tissues), a prospective pilot cohort (n = 33 stage I-IV patients), and 55 patients/donors without cancer. Hypermethylation of zinc finger and SCAN domain containing 12 (ZSCAN12) and/or oxytocin (OXT) classified EC samples from multiple noncancer samples with high diagnostic specificity/sensitivity [>97%; area under the curve (AUC) = 0.99; TCGA/GEO tissues/blood samples]. These results were confirmed in the independent retrospective cohort (AUC = 0.99). Meth-ddPCR showed a high analytical specificity (limit of blank = 2) and sensitivity (absolute lower threshold of detection = 50 pgmethDNA/mLplasma). In the pilot cohort, meth-ctDNA was detected in pretreatment plasma samples from 9/11 and 5/20 patients with advanced and non-advanced EC, respectively. 2 of 9 patients had ctDNA detected after macroscopic complete surgery and experienced progression within 6 months. No healthy donors had any copy of hypermethylated DNA detected in plasma. Meth-ddPCR of ZSCAN12/OXT allows a highly specific and sensitive detection of ctDNA in plasma from patients with EC and appears promising for personalized approaches for these patients.

Sections du résumé

BACKGROUND
No circulating biomarker is available for endometrial carcinoma (EC). We aimed to identify DNA positions universally hypermethylated in EC, and to develop a digital droplet PCR (ddPCR) assay for detection of hypermethylated circulating tumor DNA (meth-ctDNA) in plasma from patients with EC.
METHODS
DNA positions hypermethylated in EC, and without unspecific hypermethylation in tissue/cell types releasing circulating cell-free DNA in plasma, were identified in silico from TCGA/Gene Expression Omnibus (GEO) data. A methylation-specific ddPCR (meth-ddPCR) assay following bisulfite conversion of DNA extracted from plasma was optimized for detection of meth-ctDNA according to dMIQE guidelines. Performances were validated on a retrospective cohort (n = 78 tumors, n = 30 tumor-adjacent tissues), a prospective pilot cohort (n = 33 stage I-IV patients), and 55 patients/donors without cancer.
RESULTS
Hypermethylation of zinc finger and SCAN domain containing 12 (ZSCAN12) and/or oxytocin (OXT) classified EC samples from multiple noncancer samples with high diagnostic specificity/sensitivity [>97%; area under the curve (AUC) = 0.99; TCGA/GEO tissues/blood samples]. These results were confirmed in the independent retrospective cohort (AUC = 0.99). Meth-ddPCR showed a high analytical specificity (limit of blank = 2) and sensitivity (absolute lower threshold of detection = 50 pgmethDNA/mLplasma). In the pilot cohort, meth-ctDNA was detected in pretreatment plasma samples from 9/11 and 5/20 patients with advanced and non-advanced EC, respectively. 2 of 9 patients had ctDNA detected after macroscopic complete surgery and experienced progression within 6 months. No healthy donors had any copy of hypermethylated DNA detected in plasma.
CONCLUSIONS
Meth-ddPCR of ZSCAN12/OXT allows a highly specific and sensitive detection of ctDNA in plasma from patients with EC and appears promising for personalized approaches for these patients.

Identifiants

DOI: 10.1093/clinchem/hvac020 PMID: 35323926
pubmed: 35323926
pii: 6552187
doi: 10.1093/clinchem/hvac020
doi:

Substances chimiques

Biomarkers, Tumor 0
Circulating Tumor DNA 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

782-793

Commentaires et corrections

Type : CommentIn

Informations de copyright

© American Association for Clinical Chemistry 2022. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Auteurs

Guillaume Beinse (G)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.
Department of Medical Oncology, Hopital Cochin, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Paris, France.

Bruno Borghese (B)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.
Department of Gynecological Surgery, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Hopital Cochin, Paris, France.

Marie Métairie (M)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.
Department of Gynecological Surgery, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Hopital Cochin, Paris, France.

Pierre-Alexandre Just (PA)

Department of Pathology, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Hopital Cochin, Paris, France.
Université de Paris, Paris, France.

Geoffroy Poulet (G)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.

Simon Garinet (S)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.
Department of Biology, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Hopital Européen Georges Pompidou, Paris, France.

Beatrice Parfait (B)

Université de Paris, Paris, France.
Institut du Cancer Paris CARPEM, AP-HP, Fédération des Centres de Ressources Biologiques- Plateforme de Ressources Biologiques APHP, Centre de Ressources Biologiques-Site Cochin, Hôpital Cochin, Paris, France.

Audrey Didelot (A)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.

Camille Bourreau (C)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.

Natacha Agueeff (N)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.

Alexandre Lavollé (A)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.

Benoit Terris (B)

Department of Pathology, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Hopital Cochin, Paris, France.
Université de Paris, Paris, France.

Charles Chapron (C)

Department of Gynecological Surgery, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Hopital Cochin, Paris, France.
Université de Paris, Paris, France.

François Goldwasser (F)

Department of Medical Oncology, Hopital Cochin, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Paris, France.
Université de Paris, Paris, France.
Université de Paris, URP 4466, Metheho, Paris, France.

Karen Leroy (K)

Université de Paris, Paris, France.
Department of Biology, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Hopital Européen Georges Pompidou, Paris, France.

Helene Blons (H)

Université de Paris, Paris, France.
Department of Biology, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Hopital Européen Georges Pompidou, Paris, France.

Pierre Laurent-Puig (P)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.
Université de Paris, Paris, France.
Department of Biology, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Hopital Européen Georges Pompidou, Paris, France.

Valérie Taly (V)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.

Jérôme Alexandre (J)

Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris, INSERM, Paris, France.
Department of Medical Oncology, Hopital Cochin, Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Paris, France.

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