Abstract 2020: Identification of abnormal CSF1 transcripts in tenosynovial giant cell tumors and dose-dependent increase in plasma CSF1 levels in response to pexidartinib treatment
Authors: Severson Paul , West Brian L. , Tap William D. , Wainberg Zev A. , Tong-Starksen Sandra , Hsu Henry H. , Zhang Chao 
Published: September 2020

Abstract
Background: Tenosynovial giant cell tumors (TGCTs) are characterized by rearrangements of the colony-stimulating factor 1 (CSF1) gene. Dysregulated CSF1 may attract CSF1 receptor (CSF1R)-bearing mononuclear cells that form the bulk of the tumor. CSF1R inhibitors including pexidartinib have been developed and have proven to be effective therapies.
Methods: Formalin-fixed paraffin-embedded (FFPE) TGCT specimens from the phase 1 first-in-human study of pexidartinib (NCT01004861) were analyzed using a custom sequencing assay to detect CSF1 genetic alterations. The ArcherDX RNA panel (ArcherDX, Inc., Boulder, CO) consisted of 33 gene-specific primer sets specifically designed to target CSF1, including at least 1 primer set to target each exon/exon boundary as well as primer sets to tile the 3′-untranslated region (3′UTR). Plasma samples from 5 phase 1 trials of pexidartinib across multiple tumor types (NCT02777710, NCT01217229, NCT01525602, NCT01790503, NCT02452424) were assayed for CSF1 protein by solid-phase ELISA (Quantikine® Human MCSF, R&D Systems, Inc., Minneapolis, MN) at baseline and following pexidartinib (200-1200 mg).
Results: FFPE TGCT specimens (N=25) were successfully isolated, prepared into libraries, and sequenced; 8 showed evidence of gene rearrangements at the junction of CSF1 exons 5/6, and 15 showed alterations of the CSF1 3′UTR (n=23). All 25 TGCT libraries had higher CSF1 expression, with 24 exceeding 2-fold of the RNA control library. The plasma samples from 132 patients were analyzed for CSF1 protein. Pexidartinib treatment (200-1200 mg) led to a dose-dependent increase in plasma CSF1 by day 8, 15, or 29. Significant (&gt;4-fold) CSF1 elevation was observed at 600 mg or higher doses.
Discussion: All 25 analyzed TGCT study patients had tumor tissue with elevated CSF1 ligand transcripts, and 23 had CSF1 genomic alterations identified, thus confirming the TGCT etiology for which pexidartinib therapy was recently approved. The initial discovery of gross chromosomal aberrations involving the CSF1 locus used break-apart FISH probes (West et al. Proc Natl Acad Sci USA. 2006;103:690-695). Details of the CSF1 gene aberrations were obtained here using a sequencing assay suitable for FFPE specimens having partially degraded RNA. Abnormal CSF1 transcripts identified in our study are similar to those published by others (Ho et al. Genes Chromosomes Cancer. 2019[Epub]; Tsuda et al. Int J Cancer. 2019;145:3276-3284) after completion of our work, including both predicted fusion proteins and loss of 3′UTR microRNA negative regulatory sites. Increased plasma CSF1 is a useful pharmacodynamics marker of CSF1R inhibition. One potential mechanism for CSF1 plasma elevations could be the inhibition of liver macrophages, known to express CSF1R and thought to play an essential role in the normal clearance of CSF1 from circulation.
Citation Format: Paul Severson, Brian L. West, William D. Tap, Zev A. Wainberg, Sandra Tong-Starksen, Henry H. Hsu, Chao Zhang. Identification of abnormal CSF1 transcripts in tenosynovial giant cell tumors and dose-dependent increase in plasma CSF1 levels in response to pexidartinib treatment [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2020.