Activity of Type II RAF Inhibitor Tovorafenib in a Pediatric Patient With a Recurrent Spindle Cell Sarcoma Harboring a Novel SNX8-BRAF Gene Fusion

Molecular characterization of pediatric spindle cell sarcomas using comprehensive genomic profiling (CGP) has highlighted the frequent presence of activating kinase fusions in these tumors, and provides the potential for further molecular definition alongside histomorphology. Furthermore, clinically relevant targeted therapies can be identified, which may be more effective and less toxic than traditionally used chemotherapies.^1,2 NTRK (neurotrophic tyrosine receptor kinase) gene fusions have been identified as oncogenic drivers in a number of pediatric spindle cell tumors including infantile fibrosarcomas (IFS). Larotrectinib and entrectinib, US Food and Drug Administration (FDA)–approved therapies for the treatment of advanced disease harboring such rearrangements, are now in clinical use.^3,4 Recently, a subset of spindle cell tumors harboring BRAF (proto-oncogene B-Raf) fusions with striking clinical and molecular similarities to IFS have also been reported in children older than 2 years.⁵ Therapies targeting BRAF fusions in spindle cell sarcomas may prove as effective as larotrectinib in treating IFS with NTRK fusions.

BRAF is a key effector protein in the mitogen-activated protein kinase/extracellular signal regulated kinase (MAPK) pathway, which regulates cell proliferation and survival. Activating alterations in BRAF, including point mutations and gene fusions, are oncogenic drivers in many adult and pediatric solid tumors.^6,7 In the presence of BRAF fusions, such as KIAA1549-BRAF, type I BRAF inhibitors may cause paradoxical MAPK pathway activation.⁸ Therapies that instead inhibit downstream effectors of BRAF, such as the dual specificity mitogen-activated protein kinase (MEK) inhibitor (MEKi) trametinib, are more appropriate for targeting tumors harboring such fusions. Unfortunately, although responses may be observed, resistance to MEKi monotherapy generally occurs within 12-15 months.⁹

Tovorafenib (DAY101, TAK-580, MLN2480, or BIIB024), a selective, central nervous system-penetrant, type II RAF inhibitor (RAFi), is in clinical development for patients with cancers harboring an activating BRAF alteration. In biochemical assays, tovorafenib demonstrated potency against V600E-mutated BRAF monomers as well as dimeric forms of RAF and unlike type I inhibitors, tovorafenib does not induce paradoxical MAPK signaling.¹⁰ In part A of the phase I PNOC014 (Pacific Pediatric Neuro-Oncology Consortium) study (ClinicalTrials.gov identifier: NCT03429803), tovorafenib was well tolerated and induced rapid and durable responses in five of eight pediatric patients with low-grade glioma (LGG) harboring a BRAF or CRAF fusion.¹¹ Part B of this ongoing study confirmed the tolerability of tovorafenib and reported two complete responses (CRs), seven partial responses, and 15 stable diseases in 35 patients younger than 25 years with radiographically recurrent or progressive LGG or other MAPK pathway-altered tumors; of the 25 enrolled patients with tumor BRAF fusions, 10 received tovorafenib for at least 1 year (as of September 30, 2022).¹²

Tovorafenib, which is available for investigational use in both liquid and tablet oral formulations, was granted breakthrough therapy designation by the FDA for the treatment of pediatric patients with an advanced LGG harboring an activating RAF alteration, who require systemic therapy and who have either progressed after previous treatment or have no satisfactory alternative treatment options. Given the activity seen in LGGs with BRAF fusions, we explored whether tovorafenib might be an effective treatment option for a child with a recurrent spindle cell sarcoma harboring a novel SNX8 (sorting nexin 8)-BRAF gene fusion who had exhausted all treatment options including the MEKi trametinib.

Case Report

A 5-year-old boy presented with a 1-week history of fever, cough, and respiratory distress in January 2019. Because of worsening shortness of breath and tachypnea, he was referred to our emergency department for evaluation. Magnetic resonance imaging (MRI) revealed an 11.2 × 9.4 × 11.9-cm dominant right lower hemithorax mass that was partially encasing the aorta and likely arising from the posterior mediastinum, with a leftward mediastinal shift and an associated right moderate pleural effusion. He was admitted to the pediatric intensive care unit and underwent open biopsy of the mediastinal mass, which was later diagnosed as a high-grade undifferentiated spindle cell sarcoma (Fig 1). Subsequent fluorescence in situ hybridization testing indicated a BRAF gene fusion suggesting a similarity to IFS. On further staging workup, positron emission tomography-computed tomography (PET-CT) showed a hypermetabolic supraclavicular node and right-sided pleural and subcarinal lymph nodes suggesting metastatic disease rather than reactive lymph nodes. Because of the severity of the patient's clinical presentation, he was urgently started on systemic therapy with three cycles of ifosfamide and doxorubicin, with dexrazoxane cardioprotection. His symptoms improved and he was able to be discharged home. A subsequent chest CT scan showed an interval decrease in the size of the right hemithoracic mass to 4.3 × 6.6 × 4.4 cm and resolution of lymphadenopathy. The patient underwent a right thoracotomy with subtotal resection of the right chest mass, leaving a 2.1 × 2.7-cm residual soft tissue mass adjacent to the descending thoracic aorta. Radiation therapy was deferred at that time because of concerns for excessive toxicity to mediastinal structures. Meanwhile, whole-transcriptome sequencing of the tumor had revealed a novel SNX8-BRAF gene fusion, with breakpoints 3′ to exon 10 of SNX8 and 5′ to exon 9 of BRAF. The canonical BRAF protein sequence and the predicted SNX8-BRAF fusion protein, including functional domains, are shown (Fig 1).

FIG 1.

(A) Treatment summary; data cutoff November 16, 2022. (B) Structure of the SNX8-BRAF fusion protein. The structure of the canonical BRAF protein sequence (UniProtKB—P15056 [BRAF_HUMAN]: UniProt¹³) and the predicted SNX8-BRAF fusion protein, including functional domains, are shown. The SNX8 and BRAF exons, from which the protein sequences are derived, are represented by the numbers below the bars. This rearrangement is predicted to replace the N-terminal regulatory domain of BRAF with almost the entire SNX8 sequence, while leaving the BRAF kinase domain intact. (C) H&E × 10: spindle tumor cells with geographic necrosis (right upper corner); (D) HE × 20: pleomorphic tumor cells with frequent mitoses (in the center). CR, complete response; FISH, fluorescence in situ hybridization; H&E, hematoxylin and eosin; PD, progressive disease.

Although to our knowledge never previously reported, the SNX8-BRAF fusion was predicted to be a MAPK pathway activating alteration. Trametinib was started in May 2019. After the first month of treatment, the residual tumor had reduced in size, and the observed hypervascularity had resolved. A CT scan 2 months later showed no evidence of measurable tumor at the primary site. PET-CT also showed no hypermetabolic soft tissue lesion within the thorax, and no evidence of metastatic disease. In January 2021, a CT scan showed a new recurrence of a 4.0 × 3.7 × 4.6-cm left posterior mediastinal mass extending circumferentially around the aorta and impressing on the left atrium and pulmonary veins as well as abutting the T7-T8 disc space. While awaiting the results of targeted RNA-based next-generation sequencing (NGS), the patient started gemcitabine and docetaxel as second-line therapy for recurrent disease (Fig 1). After two cycles of treatment, there was no objective response on imaging and symptoms persisted.

Molecular testing reconfirmed the presence of the SNX8-BRAF fusion. Other than low-level detection of a novel ESWR1-NAB2 gene fusion, no other definitive resistance pathway alterations were identified. Functional impact of ESWR1-NAB2 is unknown; however, given the recurrence of EWSR1 aberrations in bone and soft tissue lesions, the fusion may be a trametinib-resistance mechanism.¹⁴ Given the observed clinical resistance to MEK inhibition, treatment with the RAFi tovorafenib was initiated under a compassionate use protocol in April 2021. Tovorafenib was administered at 420 mg/m² (max dose 600 mg) once weekly on a continuous 28-day schedule (days 1, 8, 15, and 22). After two cycles of tovorafenib, the patient's symptoms had resolved, and an MRI scan showed no evidence of measurable disease at the site of previously visualized tumor (Fig 2), which allowed him to proceed to safe administration of definitive proton beam radiotherapy. One week after a CR was documented, tovorafenib was held and the patient received a total dose of 6,660 centi-cobalt-gray equivalent (cCGE) in 37 fractions. Tovorafenib treatment was subsequently resumed after radiotherapy and follow-up is ongoing. As of the most recent follow-up in November 2022, the patient remains in CR. Side effects of therapy included hair hypopigmentation, grade 2 rash after the first dose of tovorafenib that resolved in a day after a dose of diphenhydramine, and grade 3 anemia requiring packed red blood cell transfusions. Radiotherapy-related adverse events included hyperpigmentation overlying the spine on the upper back with no skin breaks, and mild dysphagia, which resolved without intervention. Tovorafenib did not increase the incidence or severity of radiotherapy-related adverse events.

FIG 2.

Activity of tovorafenib. Magnetic resonance images of mediastinal mass extending circumferentially around the aorta and impressing on the left atrium and pulmonary veins are indicated by white arrows in AP and lateral views. After two cycles of treatment with tovorafenib, only a trace of nonenhancing soft tissue surrounds the descending thoracic aorta. AP, anteroposterior.

Ethics Approval and Informed Consent

The patient's parent provided written consent to the treatment protocol with tovorafenib before treatment initiation. On the same consent form, the parent gave permission for publication/presentation of any deidentified information related to his treatment course. The Children's Cancer Institute and Joseph M. Sanzari Children's Hospital at Hackensack Meridian Health had an FDA Investigational New Drug Expanded Access Protocol to administer his treatment. This Expanded Access Protocol was acknowledged by the institutions's institutional review board. The patient's parent also separately provided written consent for transfer of tumor tissue to Day One Biopharmaceuticals for additional laboratory testing.

No institutional approval was required to publish the case details.

Consent for Publication

Informed consent (both written and verbal) was obtained from patient's parent to publish this case report, which includes deidentified clinical information and imaging. Verbal consent was also provided by the patient's parent to publish the additional laboratory testing performed at an outside laboratory to identify new mutations, and possible resistance mechanisms in his relapsed tumor sample.

Discussion

The presented patient had an aggressive locally advanced spindle cell sarcoma initially not amenable to local control with gross total resection or radiotherapy. A moderate response to conventional chemotherapy meant only partial resection of the tumor was possible, leaving residual disease. Through CGP, we identified a novel oncogenic fusion, SNX8-BRAF. The durable response to tovorafenib in this patient indicates that the SNX8-BRAF gene fusion is a targetable oncogenic driver.

Treatment with the MEKi trametinib induced the first CR in this patient's disease. The remission lasted 17 months before a local recurrence occurred. With presumed resistance to MEK inhibition, the RAFi, tovorafenib, was administered. After reinduction of a CR, we were able to safely provide consolidation therapy using proton beam radiotherapy and a remission has been maintained using tovorafenib for >1.5 years. No dose-limiting toxicities were reported for our patient. Given this experience and the current improvement in accessibility of NGS at diagnosis, use of RAFi such as tovorafenib as first-line therapy for patients with advanced solid tumors harboring BRAF fusions may allow for more rapid achievement of CR, obviating the need for toxic chemotherapies and complex surgical resections. How long to continue tovorafenib once CR is achieved remains an unanswered question.

In conclusion, CGP to identify oncogenic fusions should be a standard of care for soft tissue sarcomas with IFS-like morphology. Tovorafenib is potentially effective in pediatric patients with soft tissue sarcomas harboring BRAF fusions and warrants further investigation in other BRAF fusion-driven solid tumors.

AUTHOR CONTRIBUTIONS

Conception and design: Katharine Offer, Michael C. Cox, Sandya Govinda Raju, Samuel C. Blackman

Financial support: Samuel C. Blackman

Administrative support: Michael C. Cox, Samuel C. Blackman

Provision of study materials or patients: Katharine Offer, Kunchang Song, Michael J. Goldfischer, Michael C. Cox

Collection and assembly of data: Katharine Offer, Kunchang Song, Christopher L. Corless, Carol Beadling, Tanaya Neff, Sandya Govinda Raju, Samuel C. Blackman

Data analysis and interpretation: Katharine Offer, Michael T. McGuire, Kunchang Song, Michael J. Goldfischer, Monika A. Davare, Tanaya Neff, Michael C. Cox, Sandya Govinda Raju, Samuel C. Blackman

Manuscript writing: All authors

Final approval of manuscript: All authors

Accountable for all aspects of the work: All authors

AUTHORS' DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST

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