Jose A. Carrillo

PURPOSE: The NCI-MATCH trial assigned patients with solid tumors, lymphomas, or multiple myeloma to targeted therapies on the basis of identified genetic alterations from tumor biopsies. In preclinical models, neurofibromatosis 2 ( NF2 )–inactivated tumors display sensitivity to focal adhesion kinase (FAK) inhibition. The EAY131-U subprotocol evaluated the efficacy of defactinib, a FAK inhibitor, in patients with NF2 -altered tumors. METHODS: Patients whose tumors harbored an inactivating NF2 mutation on next-generation sequencing were assigned to subprotocol U. Defactinib 400 mg was given orally twice a day until progression or intolerable toxicity. The primary end point was objective response rate (ORR), secondary end points included toxicity, progression-free survival (PFS), and 6-month PFS. RESULTS: Of 5,548 patients with sufficient tissue for genomic analysis, 57 patients were found to have NF2 alterations. Thirty-five patients ultimately enrolled and 33 were treated, with one not having central confirmation and two ineligible for outcome analysis. All patients had received previous treatment, with 52% having received three or more previous lines of therapy. The most common treatment-related toxicities were fatigue (36%), nausea (33%), and hyperbilirubinemia (27%), with 27% of patients having grade 3 toxicities. Median follow-up was 35.9 months with an ORR of 3% from one partial response in a patient with choroid meningioma. Among the 12 patients (40%) with a best response of stable disease, eight demonstrated some tumor shrinkage. Median PFS was 1.9 months, and six patients achieved a PFS >5.5 months. No correlation was identified between clinical outcomes and tumor histology or specific NF2 genotype. CONCLUSION: This protocol did not meet its prespecified primary end point. Defactinib monotherapy had limited clinical activity in this cohort of previously treated patients with solid tumors exhibiting NF2 loss.

Table S2. Individual listing of additional chordoma tissue samples collected for miR WTA.

Purpose:Chordomas are ultrarare tumors of the axial spine and skull-base without approved systemic therapy. Most chordomas have negative expression of thymidylate synthase (TS), suggesting a potential for responding to the antifolate agent pemetrexed, which inhibits TS and other enzymes involved in nucleotide biosynthesis. We evaluated the therapeutic activity and safety of high-dose pemetrexed in progressive chordoma.Patients and Methods:Adult patients with previously treated, progressive chordoma participated in an open-label, single-institution, single-arm, pilot clinical trial of intravenous pemetrexed 900 mg/m2 every 3 weeks and supportive medications of folic acid, vitamin B12, and dexamethasone. The primary endpoint was objective response rate according to RECIST v1.1. Secondary endpoints included adverse events, progression-free survival (PFS), tumor molecular profiles, and alterations in tissue and blood-based biomarkers.Results:Fifteen patients were enrolled and the median number of doses administered was 15 (range, 4–31). One patient discontinued treatment due to psychosocial issues after four cycles and one contracted COVID-19 after 13 cycles. Of the 14 response-evaluable patients, 2 (14%) achieved a partial response and 10 (71%) demonstrated stable disease. Median PFS was 10.5 months (95% confidence interval: 9 months–undetermined) and 6-month PFS was 67%. Adverse events were expected and relatively mild, with one grade 3 creatinine increased, and one each of grade 3 and 4 lymphopenia. No grade 5 adverse events, unexpected toxicities, or dose-limiting toxicities were observed. Several patients reported clinical improvement in disease-related symptoms.Conclusions:High-dose pemetrexed appears tolerable and shows objective antitumor activity in patients with chordoma. Phase II studies of high-dose pemetrexed are warranted.

Table S6. Representativeness of Study Participants

Table S5. The top 38 cfmiRs that are commonly DE in chordoma vs normal plasma samples when comparing top 100 most detected, top 100 most significant, and top 100 with highest FC.

Supplementary Figure S4. Significant cfmiRs found in plasma and tissues. A. Venn diagram showing the cfmiRs differentially expressed detected in plasma of chordoma patients that were also detected in tissue samples from chordoma patients (normalized counts >30). B. Venn diagram showing the common cfmiRs found in plasma samples considering the top 100 cfmiRs most detected, most significant changing, and most upregulated that were identified for chordoma vs normal healthy donors (NHDs). 38 cfmiRs were commonly identified as the most significantly changing, upregulated, and detected in chordoma patients.

Table S3. Plasma and tissue samples from clinical trial participants used for miR WTA.

Supplementary Figure S2. MRI and CT images of patient P04 with metastatic spinal chordoma in C-spine and lung. C-spine MRI before treatment (A-B) shows C-spine disease (arrows) and 12 months after initiation of high-dose pemetrexed (D-E) shows shrinkage of enhancing tumor on sagittal post contrast T1 sequences (A, D), sagittal T2 (B, E). Chest CT before treatment (C) showed multiple small metastases at baseline axial post contrast sequences that resolved after treatment (F).

Supplementary Figure S1. MR images of patient P05 with locally advanced clival chordoma. Brain MRI before treatment (A-C) shows left cavernous since disease (arrows), 6 months after initiation of high-dose pemetrexed (D-F), and 12 months after treatment initiation (G-J) showing shrinkage of enhancing tumor on axial post contrast T1 sequences (A, D, G), axial FLAIR (B, E, H) and axial T2 (C, F, I).

Table S4. The top 20 cfmiRs that are commonly DE in chordoma vs normal healthy donor plasma samples.