Emergency Medicine Foundation

Gene copy number (CN) amplifications and protein overexpression are common drug targets and detection relies on various methodologies, including NGS-based CN, IHC, and ISH. We investigated the pan-tumor landscape of amplifications and developed AmpRatio, a novel method of CN quantitation. Pan-tumor tissue (N=486,340) and liquid (N=85,635) samples underwent hybrid capture-based comprehensive genomic profiling. A genome-wide CN model for each sample was generated to estimate the purity, ploidy, and segment-level CN. AmpRatio was calculated by dividing gene CN/sample ploidy. A US-based de-identified clinico-genomic database was utilized to assess the relationship between ERBB2 AmpRatio and HER2 IHC/FISH and outcomes on anti-HER2 therapies. Amplifications with varying degrees of gain were reported in 38.6% of pan-tumor tissue samples, most frequently MYC (5.6%), 11q13 (5.2%), ERBB2 (5.2%), and CCNE1 (3.2%). ERBB2 AmpRatio was associated with HER2 positivity by IHC/FISH in gastroesophageal (overall percent agreement [OPA] 90%) and breast (OPA 95%) cancers. Among patients treated with anti-HER2 therapies, ERBB2 AmpRatio significantly stratified outcomes within the ERBB2-amplified and IHC-defined HER2+ and HER2-low/ultralow populations. High concordance (sensitivity 88%) of amplification detection in liquid biopsy vs tissue was associated with higher AmpRatio and ctDNA tumor fraction ≥20%. CN amplifications are prevalent and diverse biomarkers and AmpRatio is variable across genes and tumor types. ERBB2 AmpRatio is associated with outcomes to HER2-directed therapies and may have utility alongside IHC for clinical decision making. With the increasing number of therapies targeting amplifications/overexpression, it will be important to define harmonized methods for CN quantification for optimal patient selection.

The BRAF inhibitor encorafenib (Enco) plus the anti-EGFR antibody cetuximab (Cetux) improved overall survival, objective response rate, and progression-free survival in previously treated BRAFV600E-mutant metastatic colorectal cancer in BEACON, a phase III randomized trial, leading to regulatory approval for this indication. To support rapid, plasma-based testing for BRAFV600E identification, clinical validity of a ctDNA-based assay, FoundationOneLiquid CDx (F1LCDx), was assessed against the reference tumor-based clinical trial assay (CTA) in liquid biopsy-evaluable samples from BEACON and commercially obtained tissue-matched plasma samples. Pretreatment tissue samples were collected in BEACON to confirm BRAF mutational status using the central single gene PCR assay. Concordance between the CTA and liquid biopsy tests was assessed, and clinical validity of liquid biopsy testing was examined using clinical outcomes from BEACON. Of the 523 evaluable patients, 433 with matched tissue and plasma samples had CTA and F1LCDx results available (BEACON, n = 328; commercial, n = 105). A strong concordance in detecting BRAFV600E was found between F1LCDx and CTA, with a positive percent agreement of 87.2% and negative percent agreement of 97.1%. Among 42 F1LCDx-/CTA+ samples, 41 (97.6%) had ctDNA tumor fraction <1%. Among samples with ctDNA tumor fraction >1%, the positive percent agreement was 99.4% and negative percent agreement was 86.7%. Clinical outcomes with Enco plus Cetux were similar between those identified as F1LCDx+/CTA+ and CTA+ overall. This study supports using liquid biopsies as a clinically valid assay for identifying BRAFV600E alterations in patients with metastatic colorectal cancer, particularly when ctDNA tumor fraction was >1%. In the phase III BEACON trial, which established Enco plus Cetux as a standard of care for previously treated BRAFV600E-mutant metastatic colorectal cancer, mutational status was confirmed through testing of tumor tissue. To support rapid, less invasive testing for BRAFV600E in plasma, this retrospective study assessed a ctDNA-based assay and found strong concordance between the liquid biopsy test and the tumor-based assay in detecting BRAFV600E.

BackgroundMost patients with prostate cancer experience symptomatic skeletal events, leading to increased morbidity and mortality. BMAs have been approved since 2007 and recommended in mCRPC to prevent SSEs in patients with bone metastases or high-risk of osteoporotic fracture. Herein, we sought to assess real-world trends of BMA administration in patients with mCRPC.MethodsWe used the de-identified nationwide Flatiron Health electronic health record-derived database to extract patient-level data. Eligibility: patients with mCRPC with available date of mCRPC diagnosis and information on receipt of BMA. Patients were categorized into 2 cohorts based on BMA receipt. Treatment trends of BMA by year of mCRPC diagnosis were summarized using frequency and percentages. Baseline characteristics at mCRPC diagnosis (age, race-ethnicity, practice type, insurance) were compared using the Wilcoxon rank-sum and chi-squared tests.ResultsOf 24,105 patients with metastatic prostate cancer, 14,112 with mCRPC were eligible and included. A total of 7,990 (56.6%) received BMA while 6,122 (43.4%) did not. BMA receipt cohort: median age was 75 (IQR 67-81), the majority were White (61%), treated in community practice (87%) and had a commercial health plan (80%). BMA non-receipt cohort: median age was 75 (IQR 68-82), the majority were White (61%), treated in community practice (78%), and had a commercial health plan (76%). Use of BMA decreased over time from 56% in 2013 to 46% in 2024 (Table 1).ConclusionsDespite recommendations to use BMAs in patients with mCRPC and bone metastasis or high-risk of fracture, our findings reveal a low utilization rate of BMAs in mCRPC with a notable decline over time. This highlights the need to incorporate BMAs in clinical practice.Table 1Trends of BMA usage over time (2013-2024).Year, n (%)2013 N = 5492014 N = 10352015 N = 12232016 N = 13452017 N = 14412018 N = 13462019 N = 14692020 N = 13802021 N = 13522022 N = 13932023 N = 11962024 N = 383BMA receipt316 (56%)674 (65%)792 (65%)837 (62%)886 (61%)766 (57%)816 (56%)766 (56%)692 (51%)713 (51%)556 (46%)176 (46%)Denosumab190 (60.1%)450 (66.8%)557 (70.3%)599 (71.6%)606 (68.4%)533 (70%)526 (64.5%)488 (63.7%)410 (59.2%)414 (58.1%)290 (52.2%)94 (53%)Zoledronic acid120 (38%)220 (32.6%)228 (28.7%)233 (27.8%)270 (30.5%)225 (29%)281 (34.4%)273 (35.6%)277 (40%)295 (41.4%)258 (46.4%)82 (47%)Teriparatide/other bisph.6 (1.9%)4 (0.6%)7 (1%)5 (0.6%)10 (1.1%)8 (1%)9 (1.1%)5 (0.7%)5 (0.7%)4 (0.5%)8 (1.4%)0

Abstract Undifferentiated pleomorphic sarcoma (UPS) remains one of the most clinically aggressive and poorly characterized soft tissue sarcoma (STS) subtypes. To uncover distinctive molecular traits for UPS, a multi-omics analysis of UPS compared to leiomyosarcoma (LMS), and liposarcoma (LPS) was performed. Transcriptomic profiling revealed that UPS exhibits overexpression of genes encoding succinate dehydrogenase (SDH) subunits, particularly SDHB, SDHC, and SDHD, distinguishing it from LMS and dedifferentiated LPS (DDLPS). This finding was validated using the TCGA-SARC dataset. High SDHB expression in UPS was significantly associated with shorter overall survival (OS) and shorter OS from the date of first metastasis. Immunohistochemistry validated elevated SDHB protein levels in UPS and LMS relative to DDLPS. Despite overexpression of SDH subunits, metabolomic profiling demonstrated a significantly higher succinate-to-fumarate ratio in UPS, suggesting functional impairment of SDH enzymatic activity potentially due to post-translational modifications, altered assembly of SDH subunits, or imbalanced tricarboxylic acid (TCA) flux. This paradoxical phenotype of SDH overexpression with enzymatic dysfunction defines a unique molecular and metabolic subtype of UPS with prognostic significance. Recognition of this distinct SDH- associated molecular and metabolic phenotype provides insight into UPS pathogenesis, identifies a potential novel prognostic biomarker, and suggests a new avenue for metabolic-targeted therapy.

Abstract Soft tissue sarcomas (STS) histopathological classification system has several conceptual caveats, impacting prognostication and treatment. The clinical and molecular-based tools currently employed to estimate prognosis also have limitations. Clinically driven molecular profiling studies may cover these gaps. We performed DNA sequencing (DNAseq) and RNA sequencing (RNAseq), portraying the molecular profile of 102 samples of 3 of the most common STS subtypes. The RNAseq data was analyzed using unsupervised machine learning models, unravelling previously unknown molecular patterns and identifying 4 well-defined transcriptomic clusters. These transcriptomic clusters have a clear prognostic value, a finding that was externally validated. This transcriptomic cluster-based classification’s prognostic value is superior to the prognostic accuracy of currently used clinical-based (SARCULATOR nomograms) and molecular-based (CINSARC) prognostication tools. The analysis of DNAseq data from the same cohort of samples revealed a plethora of unique and, in some cases, never documented molecular targets for precision treatment across different transcriptomic clusters.

BRAF mutations are rare in biliary tract cancers (BTC), but are of interest given the recent developments in targeted therapy for BTC. We investigated the clinical outcomes in a cohort of BRAF-mutant advanced BTC treated with first-line chemotherapy. Furthermore, we investigated the genomic landscape of BRAF class I, II, and III mutations in the intrahepatic cholangiocarcinoma (iCCA) subgroup of BTC. We analyzed two nonoverlapping cohorts. We examined the genomic landscape of BRAF-mutated iCCA in a "genomic cohort" [187 class I, 82 class II, 113 class III BRAF mutants and 8,026 wildtype (WT)]. We also analyzed median progression-free survival (PFS) and overall survival (OS) on first-line chemotherapy in a separate multi-institutional "clinical cohort" of patients with BTC (including iCCA and extrahepatic cholangiocarcinoma (eCCA) and gallbladder cancer; 41 class I, 32 class II+III BRAF mutants and 1,042 WT). In the entire BTC clinical cohort, the median PFS was shorter for class I [HR, 2.11 (P < 0.001)] and class II+III [HR, 1.72 (P = 0.007)] as compared with BRAF WT. OS was also shorter in class I [HR, 2.04 (P = 0.011)] and class II+III [HR, 1.86 (P = 0.002)] as compared with BRAF WT. In the iCCA subgroup, class I alterations were mutually exclusive with FGFR2, IDH1/2, ERBB2, and KRAS mutations. Class II+III mutations appear to be mutually exclusive with FGFR2 and KRAS. In BTC, all classes of BRAF mutations are associated with a worse prognosis. BRAF mutations occur in 5% of iCCA subgroup and may be mutually exclusive with other targetable mutations.