Somatic chromosomal engineering identifies BCAN-NTRK1 as a potent glioma driver and therapeutic target

Abstract

The widespread application of high-throughput sequencing methods is resulting in the identification of a rapidly growing number of novel gene fusions caused by tumour-specific chromosomal rearrangements, whose oncogenic potential remains unknown. Here we describe a strategy that builds upon recent advances in genome editing and combines ex vivo and in vivo chromosomal engineering to rapidly and effectively interrogate the oncogenic potential of genomic rearrangements identified in human brain cancers. We show that one such rearrangement, an microdeletion resulting in a fusion between Brevican (BCAN) and Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), is a potent oncogenic driver of high-grade gliomas and confers sensitivity to the experimental TRK inhibitor entrectinib. This work demonstrates that BCAN-NTRK1 is a bona fide human glioma driver and describes a general strategy to define the oncogenic potential of novel glioma-associated genomic rearrangements and to generate accurate preclinical models of this lethal human cancer.

DNAJB1-PRKACAfusion kinase interacts with β-catenin and the liver regenerative response to drive fibrolamellar hepatocellular carcinoma

“…The oncogenic potential of the endogenous DNAJB1-PRKACA fusion in vivo was assessed. Coexpression of Cas9 with multiple single guide RNAs (sgRNAs) can be used to model chromosome translocations, inversions, and deletions by generating DNA double strand breaks (DSBs) at the breakpoints of chromosome rearrangements, which are subsequently joined by non-homologous endjoining (NHEJ) (17)(18)(19)(20)(21). While such events are rare, an oncogenic rearrangement is expected to be positively selected in vivo.…”

Immunohistochemistry with a pan‐TRK antibody distinguishes secretory carcinoma of the salivary gland from acinic cell carcinoma

“…Not only can the presence of NTRK3 rearrangement confirm the diagnosis of secretory carcinoma in the appropriate histomorphological context, but this renders the patients eligible for TRK‐targeted therapy such as treatment with larotrectinib, which was recently approved by the FDA in the USA irrespective of tumour site and histology . In addition to secretory carcinoma, NTRK fusions have been identified in most cases of infantile fibrosarcoma, cellular mesoblastic nephroma, lipofibromatosis‐like neural tumour and other paediatric mesenchymal tumours, along with a small subset of uterine sarcomas and gliomas, and rare carcinomas from the thyroid, lung, cervix, breast, and colon …”

“…Not only can the presence of NTRK3 rearrangement confirm the diagnosis of secretory carcinoma in the appropriate histomorphological context, but this renders the patients eligible for TRKtargeted therapy such as treatment with larotrectinib, which was recently approved by the FDA in the USA irrespective of tumour site and histology. 13 In addition to secretory carcinoma, NTRK fusions have been identified in most cases of infantile fibrosarcoma, 32,33 cellular mesoblastic nephroma, 34 lipofibromatosis-like neural tumour and other paediatric mesenchymal tumours, 16,17,35 along with a small subset of uterine sarcomas 36 and gliomas, 37 and rare carcinomas from the thyroid, lung, cervix, breast, and colon. 13,18,38 Although pan-TRK immunohistochemistry may serve as a useful adjunct in the screening and confirmation of NTRK alterations, 14,18 one should be aware of its strengths and limitations: pan-TRK immunohistochemistry may represent an alternative strategy to and complementary strategy for detecting NTRK1/2/ 3 rearrangements.…”

High-resolution in vivo identification of miRNA targets by Halo-Enhanced Ago2 Pulldown

“…We next tested whether the conditional Halo-Ago2 mouse could be used to identify miRNA-mRNA interactions in primary autochthonous tumors and in their tissues of origin. We first chose a mouse model of glioma driven by the Bcan-Ntrk1 gene fusion that we was recently developed in our laboratory (Cook et al, 2017). In this model, p53 fl/fl mice are injected intracranially with a mixture of two recombinant adenoviruses.…”

“…Recombinant adenoviruses used for inducing chromosomal rearrangement (Ad-BN, Ad-EA) (Cook et al, 2017;Maddalo et al, 2014) and Ad-Cre were purchased from ViraQuest. For the generation of Bcan-Ntrk1-driven gliomas, a 1:1 mixture of Ad-BN and Ad-Cre, in total ~3 x 10 9 infectious particles, was administrated to Ago2 Halo-LSL/+ ; p53 fl/fl mice (4~6 weeks old), via stereotactic intracranial injection as described in Cook et al, 2017. Gliomas were harvested approximately 80 days after injection, when mice became symptomatic.…”