BRAF V600E Mutation Research Articles

The prevalence and prognostic significance of KRAS G12C mutation in metastatic colorectal cancer.

289 Background: Kristen rat sarcoma virus ( KRAS ) mutations are reported in 40-45% of colorectal cancer (CRC), and they are associated with poor prognosis. KRAS G12C mutation is reported in 3-4% of CRC patients and may be associated with worse prognosis compared to RAS non-G12C mutations. Here, we explored the prevalence and prognostic significance of KRAS G12C mutation compared to RAS non-G12C and BRAF V600E in a cohort of CRC patients from a tertiary cancer center in the United States (US). Methods: The cBioCancer Genomics Portal was used to obtain genomic data. The prevalence of KRAS G12C mutation, RAS non-G12C ( KRAS G12D, KRAS G13D, KRAS G12V, KRAS A146T, KRAS G12A, KRAS G12S, KRAS G13C, KRAS V14I, KRAS Q61H, KRAS G12R, KRAS Q61R, KRAS K117N, NRAS Q61K , NRAS Q61R , NRAS Q61L , NRAS Q61H , NRAS G13D , NRAS G13C NRAS G13R NRAS G12D , NRAS G12C , NRAS G12V, NRAS G12V and NRAS G60V ) mutations and BRAF V600E mutations was calculated. The median overall survival (mOS) was explored in CRC (MSK, Cancer Cell 2018 cohort). Patients in this cohort were not treated with KRAS G12C targeted therapy. Survival analysis was performed using the Kaplan-Meier method with log-rank test comparisons. Results: In this cohort of patients with stage IV CRC (N=1134), the prevalence of KRAS G12C mutation in patients with stage IV CRC was 3.1%. In patients with RAS non-G12C mutations, BRAF V600E mutation, and RAS/BRAF V600E wild-type (WT), the prevalence was 41.7%, 7.5%, and 47.7% respectively. The mOS in KRAS G12C mutation, RAS non-G12C mutations, BRAF V600E mutation, and RAS/BRAF V600E WT was 65 months (m), 55m, 19m and 105m respectively. Compared to RAS non-G12C , the mOS of CRC patients with KRAS G12C was (65m vs 55m, p=0.54) . Compared to patients with BRAF V600E mutation, the mOS was better in patients with KRAS G12C (65m vs. 19m, p <0.0001) and in patients with RAS non-G12C (55m vs. 19m, p <0.0001). Conclusions: The prevalence of KRAS G12C mutation in this cohort was relatively similar to other reports at 3.1%. Consistent with several other reports, there was no statistically significant difference in the mOS between patients with KRAS G12C mutation and patients with RAS non-G12C mutations. Patients with BRAF V600E mutations had worse mOS compared to patients with KRAS G12C mutation and RAS non-G12C mutations. The reported high mOS in this cohort is possibly due to selection bias (patients able to afford and receive treatment at this tertiary center).

Cetuximab and vemurafenib plus liposomal irinotecan (II), leucovorin and fluorouracil for BRAF V600E -mutated advanced colorectal cancer (IMPROVEMENT2): A multicenter, open-label, randomized controlled trial.

TPS316 Background: Current first-line treatment regimen for advanced colorectal cancer with BRAF V600E gene mutation is chemotherapy combined with anti-angiogenic drug, but the efficacy is somewhat limited. Theoretically, targeting BRAF V600E mutation is an effective treatment strategy and has achieved success in lung cancer and melanoma. However, the objective response rate (ORR) is below 5% in colorectal cancer, suggesting that BRAF V600E mutation in colorectal cancer may have different feedback regulation mechanisms compared to other cancer types. Combining chemotherapy (such as 5-fluorouracil plus irinotecan) with BRAF/EGFR targeted therapy may potentially achieve good efficacy. Subsequently, we conducted the IMPROVEMENT (NCT03727763) study, which showed an objective response rate (ORR) of 85% and a disease control rate of 100% with this regimen, significantly higher than those with chemotherapy combined with anti-angiogenic drug. The recent BREAKWATER study showed similar trends. To further validate the efficacy and safety of this regimen, we designed a randomized controlled trial. Methods: IMPROVEMENT2 (NCT06603376) is a multicenter, open-label, randomized controlled trial in patients with histologically or cytologically confirmed advanced colorectal cancer. Adult patients who are previously untreated in the metastatic setting, have a confirmed BRAF V600E mutation, measurable disease per Response Evaluation Criteria In Solid Tumors (RECIST) version 1.1, and Eastern Cooperative Oncology Group performance status of 0-1 are eligible. Patients who received previous treatment in the adjuvant setting but experienced metastasis or recurrence within 12 months are permitted. A total of 75 eligible patients will be randomly assigned (2:1) to receive liposomal irinotecan(Ⅱ) 60 mg/m 2 , leucovorin 400 mg/m 2 , fluorouracil 2800 mg/m 2 , and cetuximab 500 mg/m 2 on day 1 of each 14-day cycle plus oral vemurafenib 720 mg twice daily, or liposomal irinotecan(Ⅱ) 60 mg/m 2 , leucovorin 400 mg/m 2 , fluorouracil 2800 mg/m 2 , and bevacizumab 5 mg/kg on day 1 of each 14-day cycle. Treatment will be continued until disease progression or unacceptable toxicity. The primary endpoint is ORR per RECIST 1.1 by blinded independent central review (BICR). Key secondary endpoints are depth of response, progression-free survival per RECIST 1.1 by BICR, overall survival, and safety. The study is actively enrolling patients. Clinical trial information: NCT06603376 .

Real-world outcomes of targeted therapies and local interventions in BRAF V600E–mutated metastatic colorectal cancer: A single-center retrospective study.

203 Background: Metastatic colorectal cancer (mCRC) patients with BRAF V600E mutations, especially those with microsatellite stable (MSS) tumors, have poor prognoses. Chemotherapy has limited efficacy in this subgroup, especially for second-line or subsequent-line treatments. Current research is increasingly focusing on the integration of targeted therapies and local interventions, but real-world evidence remains scarce, particularly from Asian cohorts. This study leverages real-world data to evaluate the impact of novel therapeutic combinations, including triplet and doublet targeted therapies, alongside local treatments in this high-risk patient population. Methods: This retrospective study includes MSS-type mCRC patients with BRAF V600E mutations treated at the Sixth Affiliated Hospital of Sun Yat-sen University between April 2014 and May 2024. Patients receiving targeted therapies were stratified into three groups: Triplet group (BRAF, EGFR, and MEK inhibitors, including Dabrafenib, Cetuximab and Trametinib), Doublet group (BRAF and EGFR inhibitors, including Dabrafenib and Cetuximab or Encorafenib and Cetuximab), and Doublet target-chemotherapy group (BRAF and EGFR inhibitors combined with chemotherapy, including Vemurafenib, Irinotecan, and Cetuximab). Primary endpoint was progression-free survival (PFS). Secondary endpoints included overall survival (OS) and objective response rate (ORR). Results: Among 239 enrolled patients, 58 received targeted therapy and 68 underwent conventional chemotherapy as second-line treatment. 63.5% (80/126) of these patients underwent local interventions, including primary tumor resection, metastasectomy, CRS±HIPEC, and liver ablation. Targeted therapy demonstrated significantly improved mPFS compared to conventional chemotherapy (5.5 vs. 4.2 months, HR = 0.44; 95% CI: 0.29-0.68, p < 0.001). OS did not differ significantly between the two treatment arms (12.7 vs. 12.1 months, HR = 0.80; 95% CI: 0.50-1.25, p = 0.330). In the triplet group, ORR, mPFS, and mOS were 21%, 5.8 months and 18.0 months, respectively, showing a trend towards enhanced efficacy compared to the other targeted therapy groups, albeit without statistical significance. Patients who received targeted therapy (n=35) or chemotherapy (n=45) in combination with local interventions demonstrated significantly prolonged OS compared to those without local therapy (mOS: 22.3 vs. 9.6 months; HR = 0.19; 95% CI: 0.09-0.42; p < 0.001 and 14.3 vs. 10.9 months; HR = 0.53; 95% CI: 0.29-0.98; p = 0.042, respectively). Conclusions: Optimal treatment for BRAF V600E mCRC remains under investigation. This study suggests that combining targeted therapies with selective local interventions may significantly improve patient survival in this challenging subgroup, warranting further prospective evaluation.

Clinical validation of plasma circulating-tumor DNA assay using highly sensitive Safe-SeqS technology for detecting RAS and BRAF V600E in metastatic colorectal cancer.

50 Background: We developed a circulating-tumor DNA (ctDNA) test assay for RAS/BRAF mutations using next-generation sequencing-based Safe-SeqS technology. The clinical performance of detecting RAS and BRAF mutations were evaluated versus approved liquid biopsy and tissue testing, respectively. Methods: Metastatic colorectal cancer (mCRC) patients (pts) were enrolled. The concordance of the RAS mutational status in ctDNA between Safe-SeqS assay and OncoBEAM RAS CRC kit, which is approved as a companion diagnostic in Japan, was evaluated using archival plasma samples. The primary endpoints were positive percent agreement (PPA) and negative percent agreement (NPA). The concordance of the BRAF V600E mutational status between plasma-Safe-SeqS assay and tissue-based testing using MEBGEN RASKET-B kit, which is approved as a companion diagnostic in Japan, was prospectively evaluated. The primary endpoints were sensitivity and specificity of Safe-SeqS assay compared to tissue-based testing. Multivariate analysis using LASSO regression model was performed to evaluate the discordance of BRAF V600E mutational status between Safe-SeqS assay and tissue-based testing. Results: In 125 eligible plasma samples, the PPA and NPA for RAS mutational status in ctDNA were 87.1% (95% confidence interval [CI]: 76.1–94.3) and 95.2% (95% CI: 86.7–99.0), respectively. On the other hand, in 103 eligible pts, the sensitivity and specificity of Safe-SeqS assay for BRAF V600E mutational status were 69.2% (95% CI: 48.2–85.7) and 98.7% (95% CI: 93.0–100.0), respectively. Multivariate analysis revealed the baseline longest diameter and the number of lesions in pts with peritoneal and/or lung metastasis were factors associated with discordance. The sensitivity for BRAF V600E mutations increased to 81.0% (95% CI: 58.1–94.6, fisher’s exact test p =0.02) when the 5 pts with lower tumor burden (peritoneal metastasis with the longest diameter <20 mm, and lung metastasis with the longest diameter <20 mm and <10 lesions, according to the previous report [1] ) were excluded. Conclusions: The clinical validity of the ctDNA assay for detecting RAS/BRAF V600E mutations using Safe-SeqS technology was confirmed in pts with mCRC. Careful attention should be paid for mCRC pts with only peritoneal and/or lung metastases having fewer metastases or smaller diameter lesions. 1. Kagawa Y, et al. Clin Cancer Res 2021.

Phase Ib/II study of fruquintinib plus 5-fluorouracil/leucovorin after progression on fruquintinib monotherapy in metastatic colorectal cancer.

128 Background: Fruquintinib is a standard third-line treatment in metastatic colorectal cancer (mCRC). However, no standard therapeutic regimen is available for mCRC patients who progressed on third-line therapy. Preclinical experiments supported a rationale for combining antiangiogenic therapy and 5-fluorouracil (5FU) in refractory mCRC with evidence for synergy. This open-label phase Ib/II study was designed to determine the safety and efficacy of fruquintinib plus 5-fluorouracil/leucovorin for mCRC patients who progressed on fruquintinib monotherapy. Methods: The enrolled patients would receive fruquintinib at a fixed dose of 4mg once daily (three weeks on, one week off) and 5FU at two dose levels (1800mg/m 2 and 2400mg/m 2 ) CIV 46 hours on day one and day 15, with leucovorin 400mg/m 2 iv 2 hours before 5FU. Treatments were repeated every 28 days. The primary endpoint was determining the recommended phase II dose (R2PD) of 5FU in phase Ib and the six-month OS rate in phase II. Secondary endpoints for phase II included objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS), and safety. Planned enrollment was 39 patients. Results: No dose-limiting toxicities occurred in the phase Ib dose-escalation study, and the R2PD of 5FU was 2400mg/m 2 . Between April 2020 and June 2024, 24 patients were enrolled in the phase II stage. The median age was 57.5 years old (from 35 to 68), and 58.33% were female. Left-sided colorectal cancer patients accounted for 75%. Sixteen (66.7%) patients harbored KRAS mutation, and one (4%) had BRAF V600E mutation. Regarding the number of lines of systemic therapy, 83.3% received this study regimen as fourth-line therapy and 16.7% as fifth-line or later therapy. As of June 30, 2024, efficacy was assessed in all 24 patients with a DCR of 62.5% (15 stable disease, nine progression disease). The median follow-up time was 16.5 months (95% CI:12.553-20.447). The primary endpoint six-month OS rate was 91.3%, the median PFS was 4.4 months (95% CI: 1.243-7.557), and the median OS was 17.3 months (95% CI: 12.892-21.708). The most common TRAEs were nausea (25%), hand-foot syndrome (16.7%), abnormal liver function (8.3%), and proteinuria (8.3%). One patient experienced grade 3 mucositis. No treatment-related death occurred. Conclusions: Fruquintinib plus 5-fluorouracil/leucovorin regimen preliminarily demonstrated promising efficacy with a tolerable safety profile for mCRC patients despite progression on prior fruquintinib monotherapy. Further investigation into this possible later-line regimen in mCRC is warranted. Clinical trial information: ChiCTR2000032640 .

The use of liquid biopsy comprehensive genomic profiling to identify the molecular landscape of patients with metastatic colorectal cancer who are candidates for anti-EGFR rechallange therapy: Findings from the CAVE-2 GOIM trial.

221 Background: In the era of precision medicine, biomarker guided therapies are necessary for patients with chemorefractory metastatic colorectal cancer (mCRC). Circulating tumor DNA (ctDNA) comprehensive genomic profiling (CGP) may contribute to the development of more effective treatments. Methods: CAVE-2 GOIM trial (ClinicalTrials.gov ID: NCT05291156) is the first randomized phase II study to assess the efficacy of avelumab plus cetuximab compared to cetuximab alone as rechallenge strategy in pre-treated plasma ctDNA RAS, BRAF WT mCRC patients. Before being enrolled in the trial, patients were selected by baseline plasma ctDNA analysis by Foundation One Liquid CDx (F1L CDx) 324 genes to identify ctDNA RAS/BRAF WT cases. Results: As of July 31th 2024, 229 (out of approximately 310) patients have been screened. A total of 1562 pathogenic variants (PV) were detected, with TP53 (86.0%), APC (84.2%), DNMT3A (30.5%) representing the most common altered genes. In these anti-EGFR pretreated patients different acquired mechanisms of resistance were observed. In particular, 72/229 (31.4%) patients had RAS or BRAF V600E PV (102 KRAS , 21 NRAS and 8 BRAF V600E mutations, respectively). Additionally, in these 72 patients, multiple RAS/BRAF V600E gene alterations (median of 1 PV, range 1-7) were observed in 41.6% cases. MAPK, RTK , and PI3K/AKT/mTOR PV were detected in 43.2%, 24.5% and 24.5% patients, respectively. Of note, the variant allele frequency of resistant PV was lower than other gene alterations, suggesting a high tumor heterogeneity as a consequence of the development and/or expansion of EGFR-inhibitor resistant cancer cell sub-clones. All patients were assessed for tumor mutational burden (TMB). Median TMB was 6 (IQR 4-10) mut/Mb, with 29.6% cases showing a TMB ≥10 mut/Mb. Finally, a total of 258 actionable genomic alterations were detected in 52,4% of patients according to the ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT). Eighty-one tier I alterations were detected in 32.3% patients, which included TMB high (29,7%), BRAF V600E (3,5%), KRAS G12C (6,5%), and RET fusions (0,4%). Conclusions: These findings support liquid biopsy-based GCP for individualized therapeutic choices in chemorefractory mCRC. Up-dated final analyses of the entire screened patient population of the CAVE-2 GOIM trial will be presented. Clinical trial information: NCT05291156 .

A cross-sectional analysis from a real-world cohort of patients with microsatellite instability colorectal cancer (MSI-CRC) with metastatic disease from the Spanish RETUD registry.

178 Background: Survival of microsatellite instability (MSI) metastatic colorectal cancer (mCRC) patients (pts) has remarkably increased with immune checkpoint inhibitors (ICI). Here, we present our real-world data regarding the management and clinical outcomes of a cohort of 214 MSI-mCRC patients included in the Spanish Group of Treatment of Digestive Tumors TTD Registry (RETUD). Methods: RETUD is a national, multicenter registry for gastrointestinal tumors from the Spanish TTD Group. In this cross-sectional analysis we evaluated a real-world cohort of MSI-mCRC pts diagnosed from 1 st January 2017 to 29 th April 2024. Baseline characteristics, treatments and treatment response are descriptively presented. Tumoral response was evaluated according to RECIST 1.1 criteria. First line progression-free survival (PFS) and overall survival (OS) analyzed by Kaplan-Meier method are presented along with 95% confidence intervals (CI). Results: Among 679 MSI-CRC pts included in RETUD, a total of 214 mCRC pts were evaluable. Pts’ age at diagnosis was 69.6 (26-96) years, and they were predominantly Caucasian (97.7%) and female (53.7%). Eastern Cooperative Oncology Group (ECOG) performance status was 0-1 for 168 (78.5%) pts. Seventeen (10.7%) pts presented Lynch syndrome. Main tumor biological characteristics are described at Table 1 and the molecular profile (when available) was: KRAS mutation (24.3%), NRAS mutation (3.5%) and BRAF v600E mutation (53.0%). Surgical resections: 158 (73.8%) pts for primary tumor and 42 (19.6%) pts for metastasis. First line systemic treatment was administered to 187 (97.1%) pts: 92 (49.2%) pembrolizumab, 83 (44.4%) chemotherapy (CT), 4 (2.1%) other ICIs, 8 (4.3%) not reported. With a median follow up period of 17.4 months, the median (95% CI) OS and first-line PFS of the total mCRC population were 32.6 (22-72.4) and 11.1 (8.2-17.9) months (m), respectively. In immunotherapy (IT) pts mOS was not achieved (22.0-NA) and PFS was 26.5 m (12.9-NA) while the mOS was 28.9 m (16.3-69.3) and PFS 7.5 (5.4-9.3) m in CT pts. The overall response rate (ORR) was 54.2% in IT pts vs. 37.3% in CT pts. Conclusions: The introduction of IT has changed the evolution of MSI-H mCRC management, offering a beneficial impact in the OS and PFS survival in contrast to other conventional therapies in a real-world context. Tumor characteristics at initial diagnosis of CRC. Stage at initial diagnosis of CRC I/II, n (%) 4 (1.9) / 26 (12.1) III/IV, n (%) 66 (30.8) / 118 (55.1) Location of primary tumor a , n (%) right colon /left colon /rectum 160 (74.8) /37 (17.3) /19 (8.9) Main metastatic location b , n (%) Liver 84 (39.3) Peritoneal 76 (35.5) Lymph 71 (33.2) Lungs 41 (19.2) a Pts with more than 1 primary tumor; the percentage may be over 100%. Data missing for 4 (1.9%) pts. b Pts with more than 1 metastatic site; the percentage may be over 100%.

Phase I/II trial of encorafenib, cetuximab, and nivolumab in microsatellite stable BRAF V600E metastatic colorectal cancer following progression on prior BRAF+EGFR targeted therapies.

182 Background: A BRAF V600E mutation, present in approximately 8-10% of all colorectal cancers (CRC), is a poor prognostic biomarker for patients with metastatic CRC. The BRAF V600E inhibitor encorafenib (E) and the anti-EGFR antibody cetuximab (C) are approved for refractory, BRAF V600E mCRC based upon on overall response rate (ORR) of 20% and median progression-free survival (PFS) of 4.2 months . A single-arm trial adding the anti-PD1 antibody nivolumab (N) to E+C in the same (BRAF-inhibitor naïve) population showed promising efficacy, with an ORR of 50% and median PFS of 7.4 months. We evaluated the efficacy of E+C+N in patients with microsatellite stable (MSS), BRAF V600E mCRC who had progressed on prior E+C. Methods: Patients with MSS, BRAF V600E mCRC with documented prior progression on E+C were eligible for treatment with E (300 mg PO daily), C (500 mg/m 2 q14 days), and N (480 mg IV q28days) were included in the study. Primary endpoint was best overall response by RECIST 1.1. Secondary endpoints were PFS, overall survival (OS), and toxicity (by CTCAE v5). Circulating tumor DNA assessment of molecular alterations in the MAPK pathway in association with response were performed by NGS. Descriptive statistics were used to summarize outcomes. Results: Among the 12 participants, none achieved a radiographic response, and 5 experienced stable disease. Disease control rate was 41.7% (95% CI, 13.8-69.6). Median PFS was 3.7 months (95% CI, 1.7-5.7), and median OS was 8.3 months (NE-NE). Four patients (16.7%) had concomitant MAPK-activating alterations at baseline, and APC , TP53 , and PIK3CA mutations were present in 25.0%, 66.7%, and 33.3% of patients, respectively. The presence of MAPK-activating mutation was not associated with disease progression (odds ratio 1.3; 95% CI 0.11-16; p=0.82). The most common grade 1-2 treatment-related adverse events (AEs) were anemia (N=5), arthralgia (N=5), rash (N=4), headache (N=4), and fatigue (N=3); 1 of the 12 patients experienced a grade 3 small bowel obstruction. Conclusions: In this pilot study, addition of N to E+C did not appear to overcome resistance to prior BRAF + EGFR targeted therapies in patients with MSS, BRAF V600E mCRC. While the addition of immunotherapy has demonstrated promising signal in early-phase clinical trials for this population, the benefit appears unlikely when offered sequentially after progression on BRAF combination therapies. Clinical trial information: NCT04017650 .

Oncomine panel testing in the clinical management of colorectal cancer: An Irish experience.

212 Background: Early onset colorectal cancer (EOCRC) is defined as colorectal cancer (CRC) in those under the age of 50. It has been hypothesized that the molecular signatures of EOCRC could differ from those of late onset CRC (LOCRC). Next Generation Sequencing (NGS) using the Oncomine Precision Assay is a useful tool to guide treatment decisions based on the presence or absence of oncogene drivers. While not all of these mutations currently influence the clinical management of CRC patients, ongoing research on the function of these genes and the development of new drugs could offer insights into patient prognosis, treatment choices and prediction of therapy resistance. Methods: Of >1500 CRC identified between 2010 and 2024, we investigated the clinical and genetic characteristics of 38 EOCRC and 41 LOCRC cases. All cases were microsatellite stable and staged I-III. NGS was performed with the Ion Torrent Genexus integrated platform using the Oncomine 45-gene Precision Assay panel. DNA hotspot mutations and copy number variations (CNVs) were assessed, followed by the classification of clinically relevant mutations using the genetic variant OncoKB database. Results: There were 38 EOCRC and 41 LOCRC cases. The age range was 27 to 49 and 50 to 91, with median ages of 44 and 72, in the EOCRC and LOCRC groups, respectively. Based on the stratification of NGS mutation levels as per the OncoKB classification, all patients in both groups (100%) had level 1 actionable mutations. NRAS wild type (WT) status was present in 100% of patients in both groups. However, differences were observed in KRAS status: 84% (32/38) of EOCRC were KRAS WT, while only 65% (27/41) of LOCRC were KRAS WT. While 3 % (n=1) of the EOCRC cohort had an ERBB2 amplification, none were detected in the LOCRC group. BRAF V600E mutations were present in 11% (4/38) of EOCRC and 12% (5/41) of LOCRC. Level 4 mutations were detected in 18% (n=7) of EOCRC, all of which were PIK3CA mutations, while these were seen in 24% (n=10) of the LOCRC group, including 9 PIK3CA mutations and 1 FGFR1 mutation. Regarding concurrent mutations, 2 patients in the EOCRC group had two mutations each: one with concurrent KRAS and PIK3CA mutations, and another with concurrent JAK2 and KRAS mutations. The LOCRC group had a higher incidence of concurrent mutations, with 8 patients affected: 6 had concurrent KRAS and PIK3CA mutations, and 2 had concurrent BRAF and PIK3CA mutations. Conclusions: Our study demonstrates that EOCRC have higher KRAS WT status and fewer concurrent mutations compared to LOCRC, who exhibit more frequent KRAS non-G12C oncogenic mutations. It also underscores the importance of routine NGS mutation panel analysis in CRC management. Additionally, identifying specific mutations in patients that relapse can guide targeted therapies, potentially improving outcomes and offering personalized treatment options.

Generating 3D brain tumor regions in MRI using vector-quantization Generative Adversarial Networks.

Medical image analysis has significantly benefited from advancements in deep learning, particularly in the application of Generative Adversarial Networks (GANs) for generating realistic and diverse images that can augment training datasets. The common GAN-based approach is to generate entire image volumes, rather than the region of interest (ROI). Research on deep learning-based brain tumor classification using MRI has shown that it is easier to classify the tumor ROIs compared to the entire image volumes. In this work, we present a novel framework that uses vector-quantization GAN and a transformer incorporating masked token modeling to generate high-resolution and diverse 3D brain tumor ROIs that can be used as additional data for tumor ROI classification. We apply our method to two imbalanced datasets where we augment the minority class: (1) low-grade glioma (LGG) ROIs from the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2019 dataset; (2) BRAF V600E Mutation genetic marker tumor ROIs from the internal pediatric LGG (pLGG) dataset. We show that the proposed method outperforms various baseline models qualitatively and quantitatively. The generated data was used to balance the data to classify brain tumor types. Our approach demonstrates superior performance, surpassing baseline models by 6.4% in the area under the ROC curve (AUC) on the BraTS 2019 dataset and 4.3% in the AUC on the internal pLGG dataset. The results indicate the generated tumor ROIs can effectively address the imbalanced data problem. Our proposed method has the potential to facilitate an accurate diagnosis of rare brain tumors using MRI scans.

Impact of synchronous vs metachronous primary tumor resection on prognosis of BRAF-V600E mutant metastatic colorectal cancer (mCRC).

304 Background: The goal of this study is to evaluate if resection of the primary tumor in synchronous versus metachronous metastatic disease predicts survival of BRAF-V600E mCRC in the era prior to combination BRAF/EGFR inhibitors. Methods: This is a retrospective study of patients treated at the Ottawa Hospital Cancer Centre with BRAF-V600E mutation mCRC who did not receive combination BRAF/anti-EGFR therapy, diagnosed with colorectal cancer prior to March 31, 2021. Demographic, clinical, pathologic and cancer characteristics were abstracted from electronic medical records. Outcomes of interest included median duration of therapy and overall survival (OS). Results: 71 patients were included with a median age of 70 years:, 37 (52%) were females, 49 (69%)had right-sided tumors and 19 (27%) were mismatch repair deficient (dMMR). The primary tumor was unresected in 22 (30%) and resected in 49 (70%), completely resected in 44 (62%), and partially resected in 5 (7%) patients. Overall, median OS was 12.9 months 95% CI (8.4, 19) with 17 months 95% CI (11, —) mOS in patients with resected primary and 6.3 95% CI (4.8, 15) months in patients with unresected primary, HR 2.48 95% CI (1.42, 4.32), p=0.001. In univariate analysis: signet ring cell (p=0.007), good performance status (p<0.001), distant lymph nodes (p<0.001), peritoneal metastasis (p=0.008), metasetectomy (p=0.002), Charlston Comorbidity Index (p=0.003) were significant prognostic factors. Synchronous versus metachronous primary tumour was not a significant prognostic factor. Conclusions: Real world data confirms that patients with BRAF-V600E mutant mCRC have poor clinical outcomes. Our analysis suggests that resection of the primary tumor did not seem to impact on survival of BRAF-V600E mutant mCRC patients. This suggests that prognosis is dictated by the systemic disease and not complications of the primary tumour itself. Of the patients with unresected primary tumour (n=21), 6 were synchronous. Metastatic status Primary Tumor Resected Primary Tumor unresected Total Synchronous 23 22 45 Metachronous 26 0 26 Total 49 22 71

Abstract B009: Abscopal effect in metastatic melanoma: generating clinical insights from radiation-induced immune response

Abstract Despite modern advancements in systemic therapies, melanoma remains a highly malignant cancer, with persistent resistance to therapies such as checkpoint inhibitors and inhibitors of mutated BRAF V600E. Current therapy for targeting metastatic melanoma remains palliative radiation therapy, particularly directly at symptomatic sites. Extraordinarily, few case studies have reported locally targeted radiation resulting in regression of distal non-targeted lesions. This rare phenomenon was coined as the abscopal effect and presents with increasing frequency due to the advancement of systemic therapy. This narrative review attempts to understand the underlying mechanisms behind the abscopal effect through clinical data from 21 melanoma patients reported in 19 case studies. Case identification focused on patients who had progressed on systemic therapy before receiving radiation. Our study observed a mean total Gy of 34 (median total 30 Gy) and mean fractionation Gy of 8 (median fractionation 7.5 Gy) with increased frequency of reported abscopal effects with incorporation of modern systemic immunotherapies. The reviewed cases suggest that combining radiation with immunotherapy may enhance systemic tumor control, though further research is required to better understand the underlying mechanisms and improve treatment outcomes. Citation Format: Baovy N. Phan. Abscopal effect in metastatic melanoma: generating clinical insights from radiation-induced immune response. [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Targeted Therapies in Combination with Radiotherapy; 2025 Jan 26-29; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(2_Suppl):Abstract nr B009.

BRAF V600E and Non-V600E Mutations in RAS Wild-Type Metastatic Colorectal Cancer: Prognostic and Therapeutic Insights from a Nationwide, Multicenter, Observational Study (J-BROS)

Background/Objectives: BRAF mutations occur in 5–10% of metastatic colorectal cancer (mCRC) cases, but their implications for prognosis and optimal treatment remain unclear. Methods: This multicenter, prospective observational study analyzed 377 RAS wild-type cases from 511 patients across 32 centers, using PCR-based methods. Results: BRAF mutations were identified in 21% (79/377) of cases, predominantly V600E (89.9%) with a minority of non-V600E (10.1%). Microsatellite instability (MSI) testing revealed MSI-high in 11.3%, exclusively among V600E cases. V600E mutations were linked to right-sided tumors, poor differentiation, and elevated CA19-9 levels. Median survival was significantly lower in V600E cases compared to BRAF wild-type (12.4 vs. 37.5 months, HR 3.25, p < 0.001) and marginally lower non-V600E cases (12.4 vs. 34.7 months, HR 0.61, p = 0.057). Chemotherapy regimens (doublet vs. triplet) and targeted treatments (bevacizumab vs. anti-EGFR) showed no significant survival differences in V600E patients. Similarly, RAS/BRAF wild-type patients had comparable survival with bevacizumab versus anti-EGFR, even for left-sided tumors. Conclusions: These findings highlight distinct clinical and prognostic profiles for BRAF V600E and non-V600E mutations, while treatment choice appears to have limited impact on survival in these subgroups or RAS/BRAF wild-type cases.

Prognostic factors and outcomes of adjuvant and first-line metastatic treatments in melanoma a Turkish oncology group study

Management of melanoma has changed significantly with the discovery of targeted therapies and immune checkpoint inhibitors (ICI). Our aim in the study is to determine which treatment alternatives, specifically dabrafenib plus trametinib and ICIs, are effective in adjuvant therapy and which treatment is effective as first-line metastatic therapy. This retrospective, multicenter study included 120 patients diagnosed with stage IIIB-IIID melanoma receiving both adjuvant and first-line metastatic treatment between 2007 and 2023. Data on clinicopathologic characteristics, treatment regimens and outcomes were collected. Objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS) and overall survival (OS) were analyzed. Patients treated with dabrafenib plus trametinib as adjuvant therapy had the longest relapse-free survival (RFS) (median: 8.3 months), followed by those treated with interferon (4.1 months) and nivolumab (1.9 months) (p = 0.002). Metastatically, the highest ORR was observed in patients treated with dabrafenib plus trametinib (54.5%), followed by ICI (52.0%) and chemotherapy (33.3%). Similarly, DCR was superior for dabrafenib plus trametinib (86.3%) compared to ICI (70.8%) and chemotherapy (66.6%). Median PFS was 9.7 months (95% CI 7.2–12.2 months) in the whole group. This was 14.3 months (95% CI 9.6–19.0 months) with ICI, 10.3 months (95% CI 4.2–16.4 months) with BRAF/MEK inhibitors and 6.3 months (95% CI 4.7–7.9 months) with chemotherapy, which was statistically significant (p < 0.001). Dabrafenib plus trametinib showed the longest median OS (53.5 months) in metastatic patients and was significantly better than chemotherapy (33.6 months) (p < 0.001). BRAF V600E mutation, RFS > 6 months, ORR are all independent factors for OS prognosis. In our study, dabrafenib plus trametinib combination was more effective in adjuvant treatment of melanoma, while immunotherapy was more effective in metastatic first-line treatment.

Recurrent Melanoma in a Patient with Chronic Lymphocytic Leukemia (CLL) Presenting with an Apparent Co-Existing NRAS and BRAF Mutation: A Diagnostic and Treatment Conundrum

Melanoma is the fifth most common cancer in the United States. The advent of immunotherapy and molecular targeted therapy has improved progression-free and overall survival in many patients with advanced disease. However, the selection of therapeutic choices requires a nuanced approach, especially when considering molecularly targeted agents. This case report highlights a diagnostic and therapeutic challenge in managing a patient with a history of chronic lymphocytic leukemia (CLL) and recurrent melanoma. Molecular testing suggested discordant BRAF V600E testing and a simultaneous NRAS G12D mutation. After a careful literature review, repetition of his molecular testing, and analysis of the timelines and results of all his molecular testing, we concluded that the BRAF V600E mutation result was falsely positive. The patient was treated with two cycles of ipilimumab (1 mg/kg) and nivolumab (3 mg/kg) as per the NADINA trial and had a complete radiographic response. He then underwent resection demonstrating a pathologic partial response ranging from 20% to 95% tumor necrosis, dependent on the satellite examined. This case report underscores the importance of precise molecular diagnostics in guiding melanoma treatment and demonstrates the complexities of managing a patient with a coexisting malignancy.

Cohort study on the treatment of BRAF V600E mutant metastatic colorectal cancer with integrated Chinese and western medicine

BACKGROUND Patients with BRAF V600E mutant metastatic colorectal cancer (mCRC) have a low incidence rate, poor biological activity, suboptimal response to conventional treatments, and a poor prognosis. In the previous cohort study on mCRC conducted by our team, it was observed that integrated Chinese and Western medicine treatment could significantly prolong the overall survival (OS) of patients with colorectal cancer. Therefore, we further explored the survival benefits in the population with BRAF V600E mutant mCRC. AIM To evaluate the efficacy of integrated Chinese and Western medicine in the treatment of BRAF V600E mutant metastatic colorectal cancer. METHODS A cohort study was conducted on patients with BRAF V600E mutant metastatic colorectal cancer admitted to Xiyuan Hospital of China Academy of Chinese Medical Sciences and Traditional Chinese Medicine Hospital of Xinjiang Uygur Autonomous Region from January 2016 to December 2022. The patients were divided into two cohorts. RESULTS A total of 34 cases were included, with 23 in Chinese-Western medicine cohort (cohort A) and 11 in Western medicine cohort (cohort B). The median overall survival was 19.9 months in cohort A and 14.2 months in cohort B, with a statistically significant difference (P = 0.038, hazard ratio = 0.46). The 1-3-year survival rates were 95.65% (22/23), 39.13% (9/23), and 26.09% (6/23) in cohort A, and 63.64% (7/11), 18.18% (2/11), and 9.09% (1/11) in cohort B, respectively. Subgroup analysis showed statistically significant differences in median OS between the two cohorts in the right colon, liver metastasis, chemotherapy, and first-line treatment subgroups (P &lt; 0.05). CONCLUSION Integrated Chinese and Western medicine can prolong the survival and reduce the risk of death in patients with BRAF V600E mutant metastatic colorectal cancer, with more pronounced benefits observed in patients with right colon involvement, liver metastasis, combined chemotherapy, and first-line treatment.

Biomarkers of resistance to anti-EGFR therapy in patients with left-sided colorectal cancer: a retrospective NGS analysis

Background: Routine analysis of KRAS, NRAS, BRAF V600 mutations, as well as MSI and HER2 guides treatment selection in colorectal cancer (CRC). Recent findings from the PRESSING and PARADIGM trials have demonstrated that the negative hyperselection of patients based on the results of comprehensive genomic profiling results in better treatment outcomes following anti-EGFR therapy. Study objective: The study aimed to retrospectively analyze the occurrence of alterations associated with potential resistance in samples from CRC patients treated with anti-EGFR therapy.Materials and methods: Patients with confirmed left-sided CRC treated with anti-EGFR therapy due to the lack of RAS / BRAFV600 mutations as per routine PCR were included in the study. FFPE samples were analyzed via NGS (Solo-test Atlas Pro, 38 genes, MSI). Samples determined as RAS / BRAFV600positive by NGS were validated with PCR.Results: A total of 111 samples were analyzed via NGS. A total of 172 alterations in 17 genes were found; alterations in any of the genes covered by the panel were found in 96 (86.5 %) samples. The variant allele frequency ranged 1.3–93.0 %. NGS identified 29 (26.1 %) samples with KRAS (n = 24), NRAS (n = 3) or BRAF p. V600E (n = 4) mutations. Confirmatory PCR testing of 16 RAS / BRAF p. V600E-positive samples resulted in 100 % agreement with NGS. Among RAS / BRAFV600negative samples, 10 (9 %) samples harbored other alterations (ERBB2 amplification, n = 3; PIK3CA, n = 2; MSI, n = 1; BRAF class II mutation, n = 1; ERBB3, n = 1). A total of 11 samples harbored more than 1 alterations associated with potential resistance. BRAF class II / III mutations were found in 4 samples, PIK3CA mutations — in 17 (15.3 %) samples (of those, 5 samples harbored mutations in exon 21).Conclusions: The results of this retrospective analysis demonstrate that a high frequency of false-positive routine PCR results may lead to incorrect indication of anti-EGFR therapy in ~ 26 % cases. Analysis of alterations beyond RAS / BRAFV600 might identify an additional 9 % of patients whose tumors are potentially resistant to anti-EGFR therapy.

A rare case of glomus tumor of uncertain malignant potential of orbit with BRAF oncogenic mutation in a young female.

A 21-year-old woman presented with progressive proptosis of the right eye with blurring of vision for the past 6 months. MRI showed an intra-orbital lesion that was T1 isointense, T2 hyperintense, and well enhancing on contrast. The patient underwent right frontal craniotomy, superior orbitotomy, and decompression of the lesion. Histopathology showed a glomus tumor with increased mitotic figures, consistent with a glomus tumor of uncertain malignant potential (GT-UMP). GT-UMP has an aggressive behavior that requires the need for adjuvant therapy following surgical excision. BRAF V600E mutation in these cases opens a new avenue for targeted therapy and precision medicine. This is the second reported case of a GT-UMP involving the orbit, and we have demonstrated BRAF V600E mutation in this case, which recurred in a short span, reiterating the aggressive nature of the tumor and the necessity of targeted therapy.

Targeting Ataxia Telangiectasia-Mutated and Rad3-Related for Anaplastic Thyroid Cancer

Background: Anaplastic thyroid cancer (ATC) is one of the most aggressive human malignancies and has a poor prognosis. Ataxia telangiectasia mutated and Rad3 related (ATR) is a key regulator for the DNA damage response and a potential target to treat cancer. Methods: We assessed the efficacy of BAY 1895344, an ATR inhibitor, in three ATC cell lines. Results: BAY 1895344 caused dose–response cytotoxicity in three ATC cell lines. BAY 1895344 induced S-phase and G2-phase arrest, activated caspase-3 activity and induced apoptosis in ATC cells. BAY 1895344 meaningfully retarded the tumor growth of an ATC xenograft model. BAY 1895344 therapy, combined with dabrafenib and trametinib, had synergism in vitro and revealed robust tumor growth suppression in vivo in two xenograft models of ATC harboring mutant BRAFV600E. Furthermore, the combination of BAY 1895344 with lenvatinib was more effective than either agent alone in a xenograft model of ATC. Conclusion: These results reveal that BAY 1895344 has potential in treating ATC.

BRAF regulates circPSD3/miR-526b/RAP2A axis to hinder papillary thyroid carcinoma progression

BackgroundPapillary thyroid carcinoma (PTC) is a common malignant tumor. BRAFV600E mutation has become a common molecular event in PTC pathogenesis. Circular RNA PSD3 (circPSD3) is known to be highly expressed in PTC. However, the bio-functional role of circPSD3 and its possible relationship with the BRAF in PTC is not clear. This study aims to probe the biofunction and molecular mechanism of circPSD3 in PTC pathogenesis.MethodsRT-qPCR was utilized to measure the expression of circPSD3 and BRAF in PTC tissues and cells. The CCK-8 and EdU assays were employed to assess cell viability and proliferation. Cell apoptosis was quantified using flow cytometry. The migratory and invasive capabilities of the cells were evaluated via wound healing and transwell assays. The interaction between RNAs was investigated using luciferase reporter assay. Additionally, xenograft tumor experiments were conducted to validate our findings in vivo.ResultsData showed that circPSD3 was highly expressed in PTC patients and cell lines. CircPSD3 was found to promote cell growth and migration and inhibit apoptosis in PTC cells. Results also revealed that circPSD3 upregulated RAP2A expression by specifically sponging miR-526b. Interestingly, inhibiting miR-526b reversed the tumorigenic properties of circPSD3 in PTC. Additionally, BRAF expression was low in PTC patients, and overexpression of BRAF hampered PTC development by downregulating circPSD3 and RAP2A while upregulating miR-526b expressions.ConclusionsOur study reveals that circPSD3 is a key regulator promoting PTC progression via the circPSD3/miR-526b/RAP2A pathway. Furthermore, we found that overexpressing BRAF, which inhibits circPSD3, significantly hampers the progression of PTC.