Specific and Sensitive Diagnosis of BCOR-ITD in Various Cancers by Digital PCR

Frontiers in Oncology

Audrey Rousseau¹  Arnaud Tauziède-Espariat²  Pascale Varlet²  Alexandre Vasiljevic³  Frédéric Fina⁴  Nicolas Macagno⁵  Doriane Barets⁵  Marie Heinisch⁵  Corinne Bouvier⁵  Carole Colin⁶  Dominique Figarella-Branger⁶  Romain Appay⁶  Daniel Pissaloux⁷  Maxime Battistella⁸  François Le Loarer⁹  Romain Perbet^1,12  Guillaume Chotard^1,13 

[1] 0Département de Pathologie Cellulaire et Tissulaire, CHU Angers, Angers, France;1Department of Neuropathology, GHU Paris-Psychiatrie Et Neurosciences, Sainte-Anne Hospital, Paris, France;2Centre de Pathologie Est, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France;3ID Solutions, Research and Development, Grabels, France;APHM, CHU Timone, Service d’Anatomie Pathologique et de Neuropathologie, Marseille, France;Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol,Marseille, France;Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France;Department of Pathology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Université de Paris, Inserm U976, Paris, France;Department of Pathology, Institut Bergonié, Bordeaux, France;Department of Translational Research and Innovation, Léon Bérard Cancer Center, Lyon, France;Institute of Pathology, CHU Lille, Lille, France;LilNCog, Lille Neuroscience and Cognition, Univ. Lille, Inserm, CHU Lille, U1172, Lille, France;Service de Pathologie, Groupe Hospitalier Pellegrin, CHU de Bordeaux, Bordeaux, France;

关键词: digital PCR assay;    BCOR-internal tandem duplication;    diagnostic marker;    HGNET-BCOR;    FFPE tissue;   

DOI  :  10.3389/fonc.2021.645512

来源: DOAJ

【 摘 要 】

BCOR is an epigenetic regulator altered by various mechanisms including BCOR-internal tandem duplication (BCOR-ITD) in a wide range of cancers. Six different BCOR-ITD in the 3’-part of the coding sequence of exon 15 have been reported ranging from 89 to 114 bp in length. BCOR-ITD is a common genetic alteration found in clear cell sarcoma of the kidney and primitive myxoid mesenchymal tumor of infancy (PMMTI) and it characterizes a new type of central nervous system tumor: “CNS tumor with BCOR-ITD”. It can also be detected in undifferentiated round cell sarcoma (URCS) and in high-grade endometrial stromal sarcoma (HGESS). Therefore, it is of utmost importance to search for this genetic alteration in these cancers with the most frequent technique being RNA-sequencing. Here, we developed a new droplet PCR assay (dPCR) to detect the six sequences characterizing BCOR-ITD. To achieve this goal, we used a single colored probe to detect both the duplicated region and the normal sequence that acts as a reference. We first generated seven synthetic DNA sequences: ITD0 (the normal sequence) and ITD1 to ITD6 (the duplicated sequences described in the literature) and then we set up the optima dPCR conditions. We validated our assay on 19 samples from a representative panel of human tumors (9 HGNET-BCOR, 5 URCS, 3 HGESS, and 2 PMMTI) in which BCOR-ITD status was known using at least one other method including RNA sequencing, RT-PCR or DNA-methylation profiling for CNS tumors. Our results showed that our technique was 100% sensitive and specific. DPCR detected BCOR-ITD in 13/19 of the cases; in the remaining 6 cases additional RNA-sequencing revealed BCOR gene fusions. To conclude, in the era of histomolecular classification of human tumors, our modified dPCR assay is of particular interest to detect BCOR-ITD since it is a robust and less expensive test that can be applied to a broad spectrum of cancers that share this alteration.

【 授权许可】

Unknown