A Phase I Study of FHD-609, a Heterobifunctional Degrader of Bromodomain-Containing Protein 9, in Patients with Advanced Synovial Sarcoma or SMARCB1-Deficient Tumors

The multisubunit Brahma-associated factor (BAF; also known as mammalian SWI/SNF) family of chromatin remodeling complexes, including canonical BAF, polybromo-associated BAF, and noncanonical BAF (ncBAF), is critical to cellular processes such as transcription, DNA repair, and replication (1). Genomic alterations involving components of these complexes have been identified in approximately 20% of cancers (2). In particular, the pathogenesis of synovial sarcoma (SS), which accounts for approximately 5% to 10% of all soft tissue sarcomas (3–6), is driven almost universally by the recurrent chromosomal translocation t(X;18) (p11.2;q11.2), which results in the fusion of the BAF component SS18 to portions of the SSX1, SSX2, or SSX4 gene products (7–9). These SS18 fusion proteins dominantly incorporate into BAF complexes and evict wild-type SS18 and SMARCB1 subunits from the BAF complex, leading to perturbed BAF complex-mediated enhancer regulation (10, 11). Additionally, biallelic loss-of-function mutations in the tumor suppressor SMARCB1 have been reported in 1% to 5% of tumors, including malignant rhabdoid tumors of the kidney, atypical teratoid rhabdoid tumors, renal medullary carcinoma, poorly differentiated chordoma, and SS (12–14). A common feature of these cancers is that the presence of an SS18–SSX fusion or biallelic inactivation of SMARCB1 is often the only detectable genetic alteration, highlighting the immense impact of epigenetic dysregulation in their pathogenesis.

Current treatment approaches for SS and SMARCB1-deficient tumors have limited efficacy, with overall response rates of approximately 15% to 30% and little impact on survival (15–17). However, because the genetic alterations in these tumors result in perturbations of canonical BAF function and aberrant transcriptional programs, SS and SMARCB1-deficient tumor cells are particularly dependent on ncBAF for survival (18, 19). Bromodomain-containing protein 9 (BRD9) is a nonenzymatic BAF subunit uniquely present in ncBAF and thus represents a selective vulnerability for SS and SMARCB1-deficient tumors (18, 19). FHD-609, a potent, selective, heterobifunctional degrader of BRD9 (20), targets this key dependency and provides a potential novel therapeutic approach in these patient populations. This multinational, multicenter phase I study evaluated the safety and tolerability of FHD-609 in patients with advanced SS and SMARCB1-deficient tumors.

Clinical study FHD-609-C-001 was a first-in-human, multinational, multicenter, open-label, nonrandomized, phase I dose escalation and expansion study of FHD-609 in patients with advanced SS or SMARCB1-deficient tumors. FHD-609 was administered by intravenous infusion over 2 hours, once or twice weekly, in 28-day cycles. This study was designed to assess the safety, tolerability, pharmacokinetics (PK), pharmacodynamics, and preliminary clinical activity of FHD-609 intravenous monotherapy in this patient population. The goal of the dose-escalation phase of the study was to determine the maximum tolerated dose (MTD) and/or recommended phase II dose(s) of FHD-609. Dose escalation occurred in two parts: Enrollment of single-patient cohorts transitioned to a traditional 3 + 3 design once one patient experienced any dose-limiting toxicity (DLT) and/or one patient experienced clinically significant grade ≥2 toxicity during the first 6 weeks of treatment. The DLT evaluation period was defined as the first 6 weeks of treatment. Dose-escalation decisions were based on the safety, clinical activity, pharmacokinetic, and pharmacodynamic data available when one (single-patient cohorts) or three DLT-evaluable patients in a given cohort had completed the DLT evaluation period. Full study design details are available in the Supplementary Data (Protocol).

A cohort-expansion phase of the study was planned to further evaluate safety and tolerability at the MTD and/or recommended phase II dose(s), but no patients were enrolled, as the study was placed on hold by the sponsor (Foghorn Therapeutics Inc.) during the dose-escalation phase because of safety concerns. The sponsor subsequently stopped the FHD-609 program.

Patients continued treatment until confirmed disease progression per Response Evaluation Criteria in Solid Tumors (RECIST) version (v) 1.1 (21), death, unacceptable toxicity, or study withdrawal. The study included a 28-day screening period. A safety follow-up visit occurred 28 days after the last dose of the study drug; survival follow-up assessments were performed every 3 months.

This study was conducted at 12 sites in four countries (United States, Spain, Italy, and France).

The study was conducted in accordance with the principles in the Declaration of Helsinki and Good Clinical Practice guidelines. The protocol was approved by the institutional review board or ethics committee at each participating site. Written informed consent was obtained from each patient, or their guardian or legal representative, before their participation.

Patients at least 16 years of age with advanced SS or SMARCB1-deficient tumors who progressed on standard therapy, who were intolerant to standard therapy, or for whom effective standard therapy was not available, were eligible. Patients were required to have measurable disease by RECIST v1.1, Eastern Cooperative Oncology Group performance status of ≤2, and adequate organ function.

Patients were excluded if they had active central nervous system metastases or prior exposure to a BRD9 degrader. Anticancer therapy within 2 weeks (or 5 half-lives) of the first dose of study treatment, systemic steroid therapy (other than stable doses for controlled chronic disease), and systemic immunosuppressive medications were not permitted. Detailed eligibility criteria are available in the Supplementary Data (Protocol).

Primary study endpoints included DLT occurrence within 6 weeks after the first dose of FHD-609 and adverse event (AE) occurrence. DLT were assessed by the principal investigator and/or sponsor according to the National Cancer Institute Common Terminology Criteria for Adverse Events, version 5.0, and were considered treatment-related (i.e., relatedness to study intervention could not be ruled out). The full definition of DLT for this study is available in the Supplementary Data (Protocol) and includes any grade ≥4 nonhematologic toxicities and grade ≥4 anemia, neutropenia, or thrombocytopenia of any duration.

Secondary study endpoints included PK and preliminary clinical activity. Serial blood samples for pharmacokinetic analysis were obtained, processed, and analyzed as described below. Treatment response was evaluated by radiographic assessment (CT and/or MRI) every 8 weeks per RECIST v1.1 (21).

Exploratory endpoints included pharmacodynamics (BRD9 expression) and exploratory biomarker analysis. Tumor biopsies were obtained at baseline, on day 15 of cycle 2 or day 1 of cycle 3, and at the end of treatment. Serial blood samples for biomarkers were obtained on days 1 and 22 of cycle 1 at predose and through 46 hours after the end of the infusion; additional predose sampling was conducted throughout cycles 1 and 2 and on day 1 of each subsequent cycle.

Tumor biopsies were processed for histology by formalin fixation and paraffin embedding at a central laboratory (PPD, Inc.). IHC was performed at Lanterne Dx on a Leica BOND RX Stainer (Leica Biosystems; RRID:SCR_025548). The following antibodies were used: BRD9 clone E4Q3F [Cell Signaling Technology, Inc., cat. No. 48306; RRID:AB_3095838], Ki67 clone K2 (Leica Biosystems, cat. No. PA0230; RRID:AB_2341199), and MYC clone Y69 (Abcam Limited, cat. No. ab32072; RRID:AB_731658). All cases were stained on a single instrument and scored by a single pathologist to avoid interlaboratory and interobserver variability. Ki67 and MYC were scored as the percentage of positive tumor cell nuclei. BRD9 was scored as H-score, using the standard formula: (1 × %_weak tumor cells) + (2 × %_moderate tumor cells) + (3 × %_strong tumor cells).

For peripheral blood mononuclear cell (PBMC) isolation from whole blood, density-gradient centrifugation was used; PBMC were cryopreserved in Cryostor CS5 (STEMCELL Technologies) at PPD, Inc., and sent to CellCarta for analysis. A cell-surface antibody cocktail was used for immunophenotyping major PBMC populations, followed by fixation/permeabilization and intracellular detection of BRD9 with the E4Q3F antibody clone. Pooled healthy donor PBMC (BioIVT) were used as controls for all batches. Samples were run on a BD LSRFortessa Cell Analyzer flow cytometer (BD Biosciences; RRID:SCR_018655), and data were analyzed using CellEngine software (CellCarta; RRID:SCR_022484). BRD9 levels were measured in T cells (CD3-positive) because this cell population was found in nonclinical studies to be the best surrogate for tumor tissue (22). BRD9 degradation in T cells was calculated by normalizing the BRD9 mean fluorescence intensity for each on-treatment time point to that patient’s baseline (cycle 1 day 1 predose) sample. BRD9 degradation was calculated for 45 patients. Eleven patients were removed from the analysis because of low baseline T-cell BRD9 levels (signal below median − 1.5 × IQR of baseline and PBMC controls) and concern for compromised sample quality.

Formalin-fixed, paraffin-embedded slides were analyzed at Discovery Life Sciences. RNA extraction was performed using the HudsonAlpha Discovery proprietary RNA/DNA dual extraction protocol. RNA amplification, rRNA reduction, and library preparation were performed using the SMARTer Stranded Total RNA-Seq Kit v2—Pico Input Mammalian (Takara Bio USA, Inc.). Paired-end sequencing was performed on an Illumina NovaSeq 6000 Sequencing System (Illumina; RRID:SCR_016387). Raw RNA sequencing (RNA-seq) data were processed by Diamond Age Data Science, LLC. Differential gene-expression analysis was performed using DESeq2 software (RRID:SCR_015687; ref. 23). Gene set enrichment analysis (GSEA; ref. 24) was performed using the GSEA program (RRID:SCR_003199) from the Molecular Signatures Database (RRID:SCR_016863; ref. 25) to identify changes to the Hallmark (26), Kyoto encyclopedia of genes and genomes (KEGG; RRID:SCR_012773; ref. 27), and Reactome (RRID:SCR_003485; ref. 28) gene sets.

Blood samples for the analysis of FHD-609 blood and plasma concentrations and calculation of PK parameters were collected at predose and at 0.25, 0.5, 1, 2, 6, 22, and 46 hours after the end of infusion on days 1 and 22 of cycle 1. Predose PK samples were also collected on days 4, 8, and 15 of cycle 1; days 1, 4, and 11 of cycle 2; and day 1 of cycle 3 and beyond. Portions of the blood samples were analyzed for FHD-609 using a validated liquid chromatography with tandem mass spectrometry method with a quantitative range of 3 to 750 ng/mL, and portions were processed to obtain plasma samples, which were analyzed for FHD-609 using a validated liquid chromatography with tandem mass spectrometry method with a quantitative range of 1 to 250 ng/mL.

The PK parameters of FHD-609 after a single dose on day 1 of cycle 1 included maximum observed concentration (C_max), time to C_max (t_max), time of last observed concentration (t_last), terminal elimination half-life (t_1/2), and area under the concentration-versus-time curve (AUC) from time 0 to 72 hours postdose (twice-weekly dosing) or from time 0 to 168 hours postdose (once-weekly dosing). The PK parameters of FHD-609 after twice-weekly or once-weekly dosing on day 22 of cycle 1 included C_max, t_max, t_last, t_1/2, and AUC from time 0 to 72 hours postdose (twice-weekly dosing) or 0 to 168 hours postdose (once-weekly dosing). Accumulation was determined by comparing the means of C_max and AUC after multiple doses on day 22 versus a single dose of FHD-609 on day 1. Noncompartmental analyses were conducted using WinNonlin (version 8.4; RRID:SCR_024504) and concentration-versus-time figures were generated in Rstudio (version 4.2.2; RRID:SCR_000432).

The safety and efficacy analysis populations included all patients who received ≥1 dose of FHD-609. The PK analysis population included all patients who received ≥1 dose of FHD-609 and had ≥1 blood sample providing evaluable pharmacokinetic data. Descriptive statistics were used for clinical, laboratory, pharmacokinetic, pharmacodynamic, and exploratory variables. This study was not designed for formal hypothesis testing, and no power analyses were done.

The human data generated in this study, including the human sequence data, are not publicly available due to patient privacy requirements but are available upon reasonable request to the corresponding author.

Across all dose levels, 55 patients treated at 12 sites received at least one dose of FHD-609 and were evaluable for safety and efficacy (Supplementary Fig. S1; Supplementary Table S1). The median time on treatment was 43 days (range, 1–463). Among the twice-weekly treatment cohorts, the median time on treatment was 77.5, 50, 50, 32, 39, and 22 days at FHD-609 5, 10, 20, 40, 60, and 80 mg twice weekly, respectively. Among the once-weekly treatment cohorts, the median time on treatment was 33.5, 43, and 50 days at FHD-609 40, 80, and 120 mg once weekly, respectively.

Demographics and disease characteristics were generally well-balanced across dose levels. The median age was 36 years (range, 19–73). Most (96.4%) patients were <65 years old, 40% were female, and approximately 64% were White. Most (96.4%) patients had an Eastern Cooperative Oncology Group performance status of 0 or 1 (Supplementary Table S1; the study population’s representativeness of the general patient population is summarized in Supplementary Table S2).

Fifty-three (96.4%) patients had a diagnosis of advanced SS; two (3.6%) patients had SMARCB1-deficient tumors (one epithelioid sarcoma and one sarcomatoid carcinoma of the renal pelvis). The median time since the diagnosis of metastatic disease was 2.0 years (range, 0.1–11.8). All patients had previously been treated with surgery, radiotherapy, and/or chemotherapy/immunotherapy (immunotherapy included T-cell therapy, cancer vaccines, checkpoint inhibitors, and monoclonal antibodies). The median number of prior lines of chemotherapy/immunotherapy was three (range, 1–8); 38 (69.1%) patients had received ≥3 prior lines of chemotherapy/immunotherapy (Supplementary Table S3). Fifty (90.9%) patients had previously been treated with anthracyclines (most commonly doxorubicin).

AE occurred in 54 (98.2%) patients. The most common (≥20%) investigator-reported AE across all dose levels were anemia (49.1%), dysgeusia (43.6%), fatigue (36.4%), dry mouth (32.7%), dyspnea (29.1%), decreased platelet count (27.3%), pyrexia (25.5%), decreased white blood cell count (23.6%), decreased neutrophil count (20%), and increased creatine kinase (20%; Supplementary Table S4). Treatment-related AE occurred in 45 (81.8%) patients; the most common (≥20%) were dysgeusia (40%), dry mouth (29.1%), fatigue (27.3%), anemia (25.5%), decreased platelet count (23.6%), and decreased white blood cell count (21.8%). Serious AE (SAE) occurrence was observed in 32 (58.2%) patients; the most common SAE was dyspnea, which occurred in five (9.1%) patients (Supplementary Table S4). No SAE of dyspnea were treatment-related. Grade ≥3 AE occurred in 40 (72.7%) patients (Supplementary Table S5). AE were managed with dose holds in 33 (60%) patients and with dose reduction in one (1.8%) patient. FHD-609 treatment was discontinued due to AE in 17 (30.9%) patients, of whom 11 were receiving a total weekly FHD-609 dose of 80 mg or higher (Supplementary Table S6). In three (5.5%) patients, the AE that led to treatment discontinuation were treatment-related and included increased creatine kinase, QT interval prolongation, repolarization abnormality, T-wave changes, torsade de pointes, and ventricular fibrillation.

One (1.8%) patient treated at the 80-mg once-weekly dose level died on study day 53 due to a venous embolism. This event was assessed by the investigator as possibly related to FHD-609 because, although the underlying malignancy remained a highly probable cause, a relationship to treatment could not be ruled out. The relatedness was confounded by the fact that the patient had recently undergone a left pneumonectomy, had been at high risk for pulmonary embolism since before the start of study treatment, and had concurrent deep vein thrombosis in the left popliteal area.

Three DLT events were observed among patients receiving FHD-609 on a twice-weekly schedule, whereas no DLT events were observed among those on a once-weekly schedule. Two patients experienced DLT at 60 mg twice weekly: One patient experienced grade 3 QT interval prolongation that progressed to grade 4, manifested as torsade de pointes and reversible cardiac arrest, and one patient experienced grade 3 syncope that was deemed a DLT by the sponsor. One patient receiving FHD-609 at 40 mg twice weekly experienced a DLT of grade 3 QT interval prolongation.

After the occurrence of the grade 3/4 QT interval prolongation in the 60-mg twice-weekly cohort, enrollment into the study was halted, and the FHD-609 dose was reduced to 40 mg twice weekly (or 80 mg once weekly) for all patients receiving FHD-609 60 mg twice weekly, 80 mg twice weekly, or 120 mg once weekly. No further DLT were reported.

The MTDs were identified as 40 mg twice weekly and the equivalent dose on a once-weekly schedule, 80 mg once weekly.

During dose escalation, T-wave abnormalities without QTc (heart rate–corrected QT interval) prolongation were noted, beginning in the 5-mg twice-weekly cohort. Investigators sought local cardiology consultation, with evaluations including cardiac injury biomarkers (troponin), echocardiography, stress testing, and cardiac CT scans as appropriate for individual patients. Given the lack of QTc prolongation and the fact that all patients remained asymptomatic, the clinical significance of the observed T-wave abnormalities was unclear and dose escalation continued. After observing DLT involving cardiotoxicity, a thorough review of the clinical data was conducted, including a case review by an external panel of expert cardiologists. Overall, of the 54 patients evaluable for assessment of QTc prolongation while receiving FHD-609, seven (13%) were reported to have had a QTc of >500 ms, and 11 (20.4%) were reported to have had an increase in QTc, from baseline, of >60 ms (Supplementary Table S4). The panel separately identified and performed a comprehensive review of the 11 of 55 (20%) patients with QTc (Fridericia formula) of >480 ms and/or an increase from a baseline of >60 ms, as identified by their electrocardiogram (ECG) overread, and/or at least one cardiovascular event, as identified by a comprehensive search strategy applied to investigator-reported AE. Based on the panel’s overread of these patients’ ECGs, all cases of QTc prolongation among these 11 patients were preceded, approximately 1 to 2 weeks earlier, by asymptomatic repolarization abnormalities, frequently in the form of T-wave inversions. Twenty-one (38.2%) patients had T-wave inversions without experiencing subsequent adverse cardiac events or additional ECG abnormalities while on study. No patients without a T-wave inversion experienced an adverse cardiovascular event. Representative on-treatment ECGs for a patient with T-wave inversion and a patient with QT interval prolongation are provided in the Supplementary Data (ECG Tracings Related to Cardiac Events).

Fifty-five patients were included in the PK analysis. FHD-609 blood and plasma exposure increased with dose on days 1 and 22 of cycle 1 across all dose levels (Fig. 1; Supplementary Table S7). The median t_max was similar across the dose levels and matrices (blood and plasma), occurring at the end of the 2-hour infusion. FHD-609 preferentially distributed into the blood, with mean blood-to-plasma ratios during cycle 1 ranging from 1.35 to 2.34 for C_max, and from 2.25 to 6.33 for AUC. The mean t_1/2 at doses from 40 to 80 mg twice weekly ranged from 31.1 to 38.3 hours in blood and from 19.6 to 26.6 hours in plasma on day 22 of cycle 1. The mean t_1/2 at doses from 80 to 120 mg once weekly ranged from 40.6 to 44 hours in blood and from 17.7 to 42.1 hours in plasma on day 22 of cycle 1. Similar half-lives of FHD-609 in blood and plasma were observed on day 1 of cycle 1 for both dosing regimens. The t_1/2 was difficult to estimate at doses of <40 mg, given the observed flat concentration-versus-time profiles in blood and plasma. No substantial accumulation of FHD-609 was observed in blood or plasma after multiple doses (geometric mean accumulation ratios <2.0 for both C_max and AUC).

Preliminary evidence of clinical activity was observed in patients with advanced SS, with one (2%) patient experiencing partial response (PR) and eight (15%) patients experiencing stable disease. Stable disease lasted longer than 6 months in two (4%) patients (Fig. 2).

The patient with a PR was a 35-year-old male with metastatic SS (SS18-SSX rearrangement confirmed by quantitative real-time polymerase chain reaction) and a history of a separate, molecularly distinct Ewing-like sarcoma. Both diagnoses were confirmed at a sarcoma reference center. The SS had previously been treated with doxorubicin and ifosfamide, leading to a complete response; pazopanib (stable disease); and trabectedin (progressive disease). Upon enrollment, the patient was treated initially with FHD-609 at 60 mg twice weekly, which was reduced to 40 mg twice weekly after approximately four cycles of treatment due to the report of QT interval prolongation in another patient in the FHD-609 60-mg twice-weekly dose group. Computed tomography scans showed an initial increase in the size of the target lesions in the setting of confounding infectious pneumonia (Fig. 3, days 4 and 9 of cycle 1). The size of the target lesions was decreased versus baseline at day 1 of cycle 5 and continued to decrease consistently throughout treatment, through the end of the patient’s participation in the study. The nontarget lesions in the pleural wall were undetectable starting on day 1 of cycle 3. A PR was first documented on day 1 of cycle 9 and maintained for four additional cycles. The total reduction in the sum of diameters of target lesions, from screening to the final on-treatment scan (day 1 of cycle 13), was 55% (Fig. 3). Plasma PK data for this patient showed no significant exposure differences relative to the other patients treated in this dose group. Pharmacodynamic data are not available for this patient, as no on-treatment biopsies were obtained. A cardiac repolarization abnormality appeared during cycle 13, resulting in the patient’s discontinuation of treatment.

BRD9 levels were assessed by IHC in tumor samples for which screening and on-treatment biopsy pairs were available (n = 17). BRD9 was found to be abundantly expressed and localized to tumor cell nuclei (Fig. 4A) in all screening samples, with a median H-score of 210 (range, 104–265). In on-treatment samples, extensive dose-dependent reductions in BRD9 levels were observed (median H-score 14; range, 0–126), with complete (100%) reduction observed in five samples across the 40-, 60-, and 80-mg twice-weekly and 80-mg once-weekly dose groups (Fig. 4B). Reductions in BRD9 levels seemed to be maintained for several days (range, 1–27 days) after the most recent dose of FHD-609. Among the two patients with stable disease lasting more than 6 months, one had an evaluable biopsy pair, which showed a 100% reduction in BRD9 levels.

BRD9 levels were also longitudinally assessed by flow cytometry in PBMC from serial blood samples obtained from 34 patients. At all dose levels, extensive reductions in BRD9 levels were observed in PBMC at the earliest time point collected (30 minutes postinfusion; Fig. 4C). Although the magnitude of the reduction was not dose-dependent, the rate of BRD9 recovery was slower at higher dose levels. The extent of the reduction in BRD9 levels in PBMC was similar after a single dose and after multiple doses (day 22 of cycle 1; Fig. 4C).

IHC for Ki67 and MYC was performed on paired tumor biopsies to examine the effect of FHD-609 treatment on tumor cell proliferation. Patients were grouped according to on-treatment BRD9 reduction (<90%, n = 8, and ≥90%, n = 9) to investigate the possibility of a relationship between the magnitude of BRD9 degradation and changes in Ki67 and MYC levels. In the ≥90% BRD9 reduction group, eight of nine on-treatment samples had reduced Ki67 levels relative to screening, whereas only three of eight samples in the <90% BRD9 reduction group had reduced Ki67 levels (Fig. 5A). The percentage of cells positive for Ki67 decreased by a median of −65.8% in the ≥90% BRD9 reduction group and increased by a median of 45.4% in the <90% BRD9 reduction group (Fig. 5B). Similarly, all nine on-treatment samples in the ≥90% BRD9 group had reduced MYC levels relative to screening, whereas only three of nine samples in the <90% BRD9 reduction group had reduced MYC levels (Fig. 5C). The percentage of cells positive for MYC decreased by a median of 82.4% in the ≥90% BRD9 reduction group and increased by a median of 32.14% in the <90% BRD9 reduction group.

To identify differentially expressed genes associated with BRD9 reduction, RNA-seq was performed on tumor biopsies, and patients were grouped according to disease and on-treatment BRD9 reduction. Groups 1 and 2 included patients with SS with ≥90% BRD9 reduction (n = 5) and <90% BRD9 reduction (n = 4), respectively. The two patients with SMARCB1-deficient tumors were assigned to a separate group (group 3) because their baseline gene expression was significantly different from that of the patients with SS (by unsupervised clustering analysis [Supplementary Fig. S2]). More extensive transcriptional changes were observed in group 1 (≥90% BRD9 reduction), which had 463 differentially expressed genes (false discovery rate–adjusted P value of <0.05). In contrast, only 58 and 78 genes were found to be differentially expressed in groups 2 and 3, respectively. By GSEA, the most strongly downregulated gene sets in group 1 involved proliferation (Hallmark E2F targets, Hallmark G2M checkpoint, Hallmark MYC targets, KEGG DNA replication, KEGG cell cycle), and protein synthesis (KEGG ribosome, reactome RRNA processing, reactome eukaryotic translation elongation; Supplementary Table S8). Additionally, certain gene sets related to cardiac physiology were upregulated in group 1.

In this article, we report results from a phase I clinical study evaluating a heterobifunctional BRD9 degrader for the treatment of patients with SS or SMARCB1-deficient tumors, selected because of the dependence of these tumors on BRD9 as a critical component of the ncBAF chromatin regulatory complex (18, 19). FHD-609 was generally tolerated in cohorts treated at doses below 60 mg twice weekly. At 60 mg twice weekly, dose-limiting QT interval prolongation was observed, which led to the declaration of the MTD of FHD-609 at 40 mg twice weekly and the equivalent weekly dose of 80 mg once weekly. An in-depth analysis of QT interval prolongation and cardiac events during FHD-609 treatment revealed that the pattern of QTc (Fridericia formula) prolongation and new-onset repolarization defects (e.g., T-wave inversion) observed in this study suggests a causal relationship between FHD-609 and the electrocardiographic findings. This finding is consistent with a recent report of the orally bioavailable BRD9 bifunctional degrader CFT8634, which, when tested in a patient population similar to the one described herein, had a similar efficacy and safety profile, including QTc prolongation and T-wave inversion (29).

It is important to note that cardiotoxicity signals were not observed in nonclinical animal studies at FHD-609 exposures that were ≥ fourfold those achieved at the highest FHD-609 dose evaluated clinically, and results from the human ether-a-go-go–related gene (hERG) assay were negative. Possible mechanisms by which FHD-609 could contribute to delayed myocardial repolarization changes and/or QTc prolongation include inhibition of hERG, or other myocardial repolarization currents, stemming from high intracellular FHD-609 concentrations in the heart as a result of tissue accumulation; the inhibition of hERG or other ion channels by a long-acting human-unique metabolite; or an effect on hERG ion channel trafficking. In the GSEA of tumor tissue from patients with ≥90% reduction of BRD9 expression, certain gene sets related to cardiac physiology were found to be upregulated. It is unknown whether these gene sets were also upregulated in cardiac tissue in these patients, and the significance of this finding is unknown. Although BAF complexes have an important role in cardiac development (30, 31), little is known about the role of BRD9 and ncBAF in the adult heart. Modulators of chromatin activity may have unexpected effects on the expression of critical genes in normal cells. Strict cardiac monitoring will be required to support the future evaluation of FHD-609.

FHD-609 monotherapy showed preliminary clinical activity in this first-in-human study of patients with SS and SMARCB1-deficient tumors. Given the advanced nature of the diseases, the heavy pretreatment of the patients enrolled, and the high unmet need of this patient population, the achievement of stable disease in eight (15%) patients, which was prolonged (>6 months) in two (4%) patients, and PR in one (2%) patient is noteworthy.

Nonclinically, FHD-609–induced BRD9 degradation in mouse models of SS resulted in decreased expression of Ki67 and MYC, as well as downregulation of cell cycle and MYC target gene sets (22). In vitro studies revealed genome-wide colocalization of BRD9 and MYC in SS cells, and loss of MYC binding to chromatin upon BRD9 degradation (32). Notably, the patients in the present study who had the greatest FHD-609–induced transcriptional changes, primarily involving gene sets associated with oncogenic growth and proliferation, were those with ≥90% BRD9 protein reduction, which directly correlated with the magnitude of Ki67 and MYC expression decrease. Complete or near-complete BRD9 reduction required an FHD-609 dose of 40 mg twice weekly or higher. In fact, the patient with a PR was initially treated at 60 mg twice weekly, and this response was obtained after eight cycles of FHD-609 therapy. These data suggest that deeper and more durable responses may require complete or near-complete BRD9 reduction, sustained over a substantial period of time. This in turn requires prolonged exposure to high concentrations of FHD-609, which most patients may find difficult to tolerate, or which may not be adequate when disease kinetics are accelerated. It is tempting to speculate that an improved efficacy profile may be achieved by developing more potent and better-tolerated BAF degraders or through combinations with other agents with orthogonal mechanisms of action.

This first-in-human phase I study successfully identified the MTD for a selective heterobifunctional BRD9 degrader in patients with SS or SMARCB1-deficient malignancies and demonstrated extensive, dose-dependent BRD9 reduction in target tumor tissue. Although these results validate using protein degraders to selectively target epigenetic proteins in oncology, the observed clinical activity was modest. Similar results were observed with CFT8634, another BRD9 degrader evaluated in the clinic; the first-in-human dose-escalation study was stopped because of insufficient single-agent efficacy (33).

Given the pharmacodynamic impact of FHD-609 on target tissue, its limited single-agent activity, and the high unmet need of this patient population, further studies involving BRD9 degradation strategies will require either combinations with other active therapies used in the treatment of SS, or novel approaches such as antibody-degrader conjugates that maximize drug delivery to tumor tissue in a more targeted fashion. Regardless, the cardiac signal described herein will require stringent monitoring.

J.A. Livingston reports grants and nonfinancial support from Foghorn Therapeutics Inc. during the conduct of the study, and grants and nonfinancial support from Exelixis and Genentech outside the submitted work. J.-Y. Blay reports other support from Foghorn Therapeutics Inc. during the conduct of the study. C. Valverde reports other support from Foghorn Therapeutics Inc. during the conduct of the study; grants and personal fees from PharmaMar, Boehringer, Bayer, Deciphera, and Lilly; and personal fees from Phillogen outside the submitted work. M. Agulnik reports personal fees from Boehringer Ingelheim, Deciphera, and Aadi outside the submitted work. M. Gounder reports other support from Foghorn Therapeutics Inc. during the conduct of the study; personal fees and other support from Ayala, Epizyme, Kura Oncology, and Rain Oncology; personal fees from Aadi Biosciences, Boehringer, Ikena, Regeneron, and TYME; and other support from GSK and SpringWorks outside the submitted work. A. Le Cesne reports personal fees from Deciphera outside the submitted work. M. McKean reports grants from Foghorn Therapeutics Inc. during the conduct of the study; grants from Aadi Biosciences, Alpine Immune Sciences, Arcus Biosciences, Arvinas, Ascentage Pharma Group, ASCO, Astellas, Aulos Bioscience, Bayer, Bicycle Therapeutics, BioMed Valley Discoveries, BioNTech, Boehringer Ingelheim, C4 Therapeutics, Daiichi Sankyo, Dragonfly Therapeutics, EMD Serono, Epizyme, Erasca, Exelixis, G1 Therapeutics, Genentech/Roche, Gilead Sciences, GlaxoSmithKline, IconoVir Bio, IDEAYA Biosciences, Ikena Oncology, ImmVira Pharma, Infinity Pharmaceuticals, Jacobio Pharmaceuticals, Jazz Pharmaceutical, Kechow Pharma, Kezar Life Sciences, Kinnate BioPharma, Krystal Biotech, MedImmune, Mereo BioPharma, Metabomed, Moderna, NBE Therapeutics, Nektar, Novartis, NucMito Pharmaceuticals, OncoC4, Oncorus, OnKure, PACT Pharma, Plexxikon, Poseida, Prelude Therapeutics, Pyramid Biosciences, Remix Therapeutics, Sapience Therapeutics, Scholar Rock, Seattle Genetics, Synthrox, Takeda Pharmaceuticals, Teneobio, Tempest Therapeutics, Tizona Therapeutics, TMUNITY Therapeutics, TopAlliance Biosciences, and Xilio; grants and other support from Bristol Myers Squibb, Daiichi Sankyo, Moderna, Pfizer, and Regeneron; and other support from AbbVie, Castle Biosciences, IQVIA, Merck, Pierre Fabre, and Revolution Medicine outside the submitted work. M.J. Wagner reports personal fees from Deciphera, Aadi, PharmaEssentia, and Epizyme and nonfinancial support from Adaptimmune outside the submitted work. S. Stacchiotti reports grants and other support from Foghorn Therapeutics Inc. during the conduct of the study; grants from Adaptimmune, Abbisko, Advenchen, Epizyme, Hutchinson, Inhibrx, and SpringWorks; and personal fees from GlaxoSmithKline, Agenus, Bayer, Boehringer, Deciphera, Daiichi Sankyo, Gentili, Ikena, Ipsen, NEC OncoImmunity, Novartis, Pharma Essentia, PharmaMar, Regeneron, and Servier outside the submitted work. A. Quintás-Cardama reports other support from Foghorn Therapeutics Inc. during the conduct of the study. S.A. Reilly reports other support from Adaptimmune Therapeutics outside the submitted work. D. Hickman reports other support from Foghorn Therapeutics Inc. outside the submitted work. A. Ballesteros-Perez reports other support from Certara during the conduct of the study. A. Khalil reports other support from Agios Pharmaceuticals outside the submitted work. M.P. Collins reports personal fees from Foghorn Therapeutics Inc. during the conduct of the study and has a patent for Methods of Treating Cancer pending. K. Horrigan reports personal fees from Foghorn Therapeutics during the conduct of the study. A. Lefkovith reports other support from Repare Therapeutics Inc. and Syros Pharmaceuticals Inc. outside the submitted work. S. Innis reports other support from Foghorn Therapeutics Inc. outside the submitted work. A.J. Lazar reports personal fees and nonfinancial support from Foghorn Therapeutics Inc. during the conduct of the study. G.M. Cote reports honorarium from Gilead Sciences; consultant role with Chordoma Foundation; scientific advisory board membership with Ikena Oncology, C4 Therapeutics, and Daiichi Sankyo; clinical trial investigator role with Servier Pharmaceuticals, PharmaMar, MacroGenics, Eisai, Merck KGaA/EMD Serono Research & Development Institute, SpringWorks Therapeutics, Repare Therapeutics, Foghorn Therapeutics Inc., SMP Oncology, Jazz Pharmaceuticals, Rain Oncology, BioAtla, Inhibrx, Ikena Oncology, C4 Therapeutics, Kronos, Bavarian Nordic, and Pyxis Oncology; and travel expenses from PharmaMar. A.J. Wagner reports grants and nonfinancial support from Foghorn Therapeutics Inc. during the conduct of the study, and grants and personal fees from Aadi Bioscience, Boehringer Ingelheim, Cogent Biosciences, Daiichi Sankyo, Deciphera, and Servier; personal fees from BioAlta, Kymera, and PharmaEssentia; and grants from Rain Therapeutics outside the submitted work. No disclosures were reported by the other authors. 

J.A. Livingston: Conceptualization, resources, supervision, investigation, writing–review and editing. J.-Y. Blay: Resources, supervision, investigation, writing–review and editing. J. Trent: Conceptualization, resources, supervision, investigation, writing–review and editing. C. Valverde: Resources, supervision, investigation, writing–review and editing. M. Agulnik: Resources, supervision, investigation, writing–review and editing. M. Gounder: Resources, supervision, investigation, writing–review and editing. A. Le Cesne: Resources, supervision, investigation, writing–review and editing. M. McKean: Resources, supervision, investigation, writing–review and editing. M.J. Wagner: Resources, supervision, investigation, writing–review and editing. S. Stacchiotti: Resources, supervision, investigation, writing–review and editing. S. Agresta: Conceptualization, formal analysis, supervision, methodology, writing–review and editing. A. Quintás-Cardama: Formal analysis, supervision, writing–original draft, writing–review and editing. S.A. Reilly: Conceptualization, formal analysis, supervision, methodology, writing–original draft, writing–review and editing. K. Healy: Data curation, project administration, writing–review and editing. D. Hickman: Formal analysis, supervision, writing–review and editing. T. Zhao: Data curation, formal analysis, visualization, methodology, writing–review and editing. A. Ballesteros-Perez: Data curation, formal analysis, methodology, writing–review and editing. A. Khalil: Visualization, writing–original draft, writing–review and editing. M.P. Collins: Data curation, formal analysis, investigation, visualization, methodology, writing–original draft, writing–review and editing. J. Piel: Conceptualization, data curation, formal analysis, supervision, methodology, writing–review and editing. K. Horrigan: Data curation, investigation, methodology, writing–review and editing. A. Lefkovith: Data curation, investigation, methodology, writing–review and editing. S. Innis: Conceptualization, supervision, project administration, writing–review and editing. A.J. Lazar: Formal analysis, writing–review and editing. G.M. Cote: Conceptualization, resources, supervision, investigation, writing–review and editing. A.J. Wagner: Conceptualization, resources, supervision, investigation, writing–review and editing.

This study was funded by Foghorn Therapeutics Inc. We thank the patients, study investigators, and staff who participated in this study. The authors would also like to thank Mia Bosinger for performing analyses that helped identify differentially expressed genes associated with BRD9 reduction.