PFS and OS by detection of BRAF V600 alterations in ctDNA at (A and B) baseline and (C and D) on treatment. Only patients with BRAF V600 alteration detections at baseline are shown in C and D. Bini, binimetinib; D, detectable; Enco, encorafenib; ND, nondetectable; Vemu, vemurafenib.

Supplementary Figure S5 shows redox metabolite levels in wildtype and SelenoO deficient cell lines.

PURPOSE:Treatment with encorafenib ± binimetinib is associated with improved survival versus vemurafenib in patients with BRAF V600E/K-mutant advanced melanoma. We retrospectively analyzed genomic and transcriptomic data from the phase III COLUMBUS trial to identify molecular correlates of benefit with encorafenib ± binimetinib. EXPERIMENTAL DESIGN:In COLUMBUS, patients with BRAF V600E/K-mutant locally advanced, unresectable, or metastatic melanoma (n = 921) were randomized to receive encorafenib plus binimetinib, encorafenib, or vemurafenib. We used whole-exome sequencing (n = 666), whole-transcriptome sequencing (RNA sequencing; n = 514), and assessment of circulating tumor DNA (ctDNA) at baseline (n = 336) and on treatment (cycle 2 day 1, n = 184) to evaluate biomarker associations with progression-free and overall survival. RESULTS:Survival benefits with encorafenib plus binimetinib versus vemurafenib were greatest in patients with higher tumor mutational burden (TMB) and those with evidence of tumor immune infiltration (i.e., higher cytolytic score, PD-L1 expression, or IFNγ gene signature scores). Clustering of gene expression profiles identified three tumor subgroups, including an "immune" subgroup associated with improved survival. Detection of BRAF V600 alterations in baseline ctDNA was associated with shorter survival; clearance of BRAF V600 alterations at cycle 2 day 1 was associated with improved survival across arms. CONCLUSIONS:The greatest benefits of encorafenib plus binimetinib were observed in patients with evidence of high TMB and/or tumor-immune infiltration, suggesting potential immune contributions to efficacy, which were not observed with vemurafenib. BRAF V600 detectability in ctDNA seems to have utility as a marker of prognosis and response in this population.

Supplementary Figure S4 depicts characterization of SelenoO deficient cell lines

LBA9517 Background: PIVOTAL (NCT02938299) is an open-label, randomized, multicenter, phase 3 trial evaluating daromun as a neoadjuvant intralesional (IT) therapy for resectable, locally advanced stage III melanoma. The trial enrolled 256 efficacy-evaluable patients (pts) in the EU and met its primary endpoint, demonstrating a statistically significant improvement in recurrence-free survival (RFS; HR = 0.59; p = 0.005) for daromun versus upfront surgery, at a median follow-up (FU) of 21 months from randomization (Kähler et al, Ann Onc 2025, 36, 1166). Methods: Pts with skin and/or lymph node metastatic melanoma amenable to complete surgical resection were randomized (1:1) to receive 4 weekly IT injections of daromun (13 Mio IU of L19IL2 and 400 μg of L19TNF) followed by surgery or upfront surgery alone. Prior surgery, radiotherapy (RT) and/or systemic therapies (ST) were permitted, as well as any approved adjuvant treatment post-surgery.The primary endpoint was RFS, the secondary endpoints included DMFS, OS and safety. An event-free survival (EFS) sensitivity analysis was conducted, considering progression to unresectable melanoma before surgery, recurrence of the disease, or death due to melanoma or treatment as events. Results: An updated primary outcome analysis at a median FU of over 36 months from randomization (database cut-off Nov. 29, 2025) confirmed a clinically relevant improvement in RFS (HR = 0.60; p = 0.003) for daromun versus upfront surgery. The EFS sensitivity analysis carried out in the overall population was consistent with the RFS results (HR = 0.66; 95% CI = 0.47-0.92).The PIVOTAL trial included two clinically distinct subgroups: pts with newly diagnosed disease (n = 32; 12%) and pts with recurrence(s) after surgery and/or systemic (neo)adjuvant treatment (n = 224; 88%). Among the recurrent cohort, 86 pts (38.3%) had received and failed previous ST, while 138 pts (61.6%) had only received surgery/RT. Sensitivity EFS analyses were also performed in i) the recurrent cohort (HR = 0.59; 95% CI = 0.41-0.85), ii) the subgroup of pts in the recurrent cohort who had only received previous surgeries and/or RT (HR = 0.55; 95% CI = 0.34-0.89), and iii) the pts subgroup in the recurrent cohort who received prior ST (HR = 0.63; 95% CI = 0.36-1.08 ). The rate and type of treatment-related adverse events at a longer FU were consistent with previous reports, and no new safety risks were identified. Conclusions: With longer FU the highly significant reduction in the risk of recurrence or death with neoadjuvant daromun in pts with locally advanced stage III melanoma is confirmed. The sensitivity EFS analyses provide consistent, confirmatory evidence of daromun’s efficacy across the entire trial population and, more importantly, in the subgroup of pts with recurrent disease, regardless of any prior ST. No new safety signals were reported. Clinical trial information: NCT02938299 .

Supplementary Figure S7 shows mass spectra of SdhA and Aco2

Supplementary Figure S6 depicts markers of subcellular fractionation used to isolate crude mitochondria.

9576 Background: Patients with resected stage III BRAF V600 mutated melanoma can be treated with combined dabrafenib and trametinib (D/T) with significant improvement of recurrence-free survival (RFS). The results of the pivotal Combi-AD study showed overall survival (OS) improvement only for patients with BRAF V600E mutations, while for V600K there was even an OS impairment as compared to placebo, although not statistically significant. Methods: We analysed EUMelaReg data for patients with adjuvant D/T therapy for resected stage III melanoma. Only patients with V600E and V600K mutations were selected, where n=93 from a total of 1,033 patients (9.0 %) harboured V600K. Results: Demographics of patients with V600K mutations differed significantly for age (67 vs. 58 years, p <0.001) and a higher proportion of males (67.0% vs. 54.6%, p=0.03) at baseline. Other baseline variables, including substage, were not significantly different. One year of treatment was completed in 51.6% for V600K, and 62.8% for V600E, respectively, while with V600K mutations 22.6% of the patients stopped for toxicity (vs. 18.8% with V600E), and 10.8% for disease recurrence (vs. 6.9%), which was not statistically significant. After a median follow-up of 41.7 (V600K) and 41.2 (V600E) months, Kaplan-Meier analysis estimated 4-year overall survival of 75.7% for V600K compared to 77.8% for V600E. The 4-y-RFS estimates were 48.3% for V600K and 47.0% for V600E. These differences were not statistically significant. Cox regression analysis revealed no different results when adjusted for demographic co-variates, including age and sex, for RFS and OS, respectively. Conclusions: It appears that V600E and V600K mutations are not associated with a different outcome from adjuvant treatment with combined D/T. The findings offer no explanation for differences found in the Combi-AD trial, although part of these differences also resulted from a different natural course of V600K mutated melanomas the placebo group. A longer follow-up will help to further confirm these results and also analyse the possible role of further treatments in the metastatic setting. Baseline characteristics and outcome. V600E(N=940) V600K(N=93) P-value SEX 0.035 Female 426 (45.3%) 31 (33.3%) Male 514 (54.7%) 62 (66.7%) AGE <0.001 Mean (SD) 57.4 (13.8) 65.6 (11.9) Median [Min, Max] 58.0 [17.0, 90.0] 67.0 [28.0, 87.0] ECOG 0.1 0 846 (90.0%) 82 (88.2%) 1 51 (5.4%) 8 (8.6%) 2 5 (0.5%) 2 (2.2%) Baseline Stage 0.34 III 8 (0.9%) 1 (1.1%) IIIA 126 (13.4%) 7 (7.5%) IIIB 293 (31.2%) 29 (31.2%) IIIC 470 (50.0%) 54 (58.1%) IIID 43 (4.6%) 2 (2.2%) STAGE III DIAGNOSIS TYPE 0.96 Primary Diagnosis 679 (72.2%) 68 (73.1%) Relapse 260 (27.7%) 25 (26.9%) SUBTYPE 0.06 SSM 358 (38.1%) 26 (28.0%) NMM 315 (33.5%) 44 (47.3%) NOS 207 (22.0%) 18 (19.4%) MUP 49 (5.2%) 4 (4.3%) OUTCOME 4-Year RFS (95%-CI) 0.47 (0.43; 0.51) 0.48 (0.38; 0.61) 0.94 4-Year OS (95%-CI) 0.78 (0.75; 0.81) 0.76 (0.65; 0.88) 0.94

Background Existing tools for virus variant identification can pinpoint the most abundant virus variant in a sequencing sample. However, patients can be infected by more than one variant of the same virus species or strain, for example by multiple variants of SARS-CoV-2. This leads to the more complicated problem of virus variant quantification from samples containing virus mixtures. Results We report on improvements of Orthanq, our generic tool for haplotype quantification, and show how it can be applied to perform uncertainty aware quantification of virus variants. We evaluate this ability on simulated and real SARS-CoV-2 and HIV-1 virus mixture datasets and show that Orthanq outperforms other state of the art approaches. Conclusions Orthanq performs identification and uncertainty-aware quantification of known virus variants of any virus species, in particular also in samples with mixed infections. With extensive built-in visualizations and reporting of alternative solutions with posterior densities, users can easily evaluate the uncertainty of the results.

DNA methylation provides a stable record of cellular identity, capturing epigenetic programs that distinguish specialized cell states despite a shared genome. Because malignant transformation and tumour progression are accompanied by extensive epigenetic remodeling, we hypothesized that the methylome of melanocytic lesions contains biologically and clinically relevant information for both diagnosis and disease progression. In a cohort of 1,001 tissue samples prospectively collected across eight German university hospitals profiled using Illumina Infinium MethylationEPIC arrays, we compared machine-learning models based on selected Cytosine phosphate Guanine (CpG) methylation sites with models incorporating biology-guided features, including epigenetic age acceleration, cell type composition and copy-number variation burden. In an external test set, the best diagnostic classifier was CpG-based and distinguished melanocytic nevi, noninvasive melanoma and invasive melanoma with a macro-averaged area under the receiver operating characteristic curve of 0.919 (95

The prospective, German NICO study (ClinicalTrials.gov identifier: NCT02990611) evaluated real-world effectiveness and safety with nivolumab plus ipilimumab or nivolumab alone (any-line) in patients with advanced melanoma with/without melanoma brain metastasis (MBM). A total of 755 patients treated with nivolumab plus ipilimumab (n = 486; median follow-up, 46.8 months) or nivolumab alone (n = 269; median follow-up, 38.7 months) were enrolled. Baseline characteristics differed between the treatment groups, with the nivolumab plus ipilimumab group being younger and having poorer prognostic factors. At baseline, 221 patients (29.3%) had MBM, among whom 15 patients had symptomatic MBM based on dexamethasone use. In patients with/without MBM receiving first-line nivolumab plus ipilimumab, objective response rates (ORRs) were 46.2% and 54.0%, respectively; 3-year overall survival (OS) rates were 34.0% and 47.0%. In patients with/without MBM receiving first-line nivolumab alone, ORRs were 61.5% and 55.1%, respectively; 3-year OS rates were 42.7% and 47.8%. In a 3-month landmark analysis, patients with MBM with a complete/partial response demonstrated 3-year OS rates of 71.9% with nivolumab plus ipilimumab and 89.6% with nivolumab alone. Three-year OS rates were 42.2% and 20.0% with asymptomatic and symptomatic MBM, respectively. There were no substantial differences in the rates of serious grade 3/4 treatment-related adverse events between patients with/without MBM. HRQoL was stable. Results from this real-world study show that a substantial proportion of patients with MBM derive long-term benefit from nivolumab plus ipilimumab or nivolumab alone, particularly those with asymptomatic MBM.

Abstract Adverse drug effects remain a major barrier to safe and effective cancer therapy, underscoring the need for tools that predict treatment-related toxicities. We analyzed multimodal real-world data from 14,596 cancer patients across 38 cancer entities, encompassing 330 clinical, tumor, and imaging characteristics, along with 89 anticancer agents. Hematological adverse events (HAE), defined by nadirs of hemoglobin, leukocyte, neutrophil, and platelet values within two months of treatment initiation, were highly prevalent (87.7%; 33.1% severe). We developed Toxix , an explainable artificial intelligence (xAI) framework modeling interactions between patient characteristics and drug combinations. Toxix achieved strong predictive performance for severe toxicities (median AUROC 0.85 for anemia; >0.76 for leukopenia, neutropenia, and thrombocytopenia) and was validated in an external cohort of 2,768 patients with non-small cell lung cancer. Model explainability enabled systematic characterization of drug-patient interactions underlying HAEs. Toxix provides a real-world informed framework for personalized and toxicity-aware cancer therapy planning.

Characterization of tumor samples to identify candidate molecular subtypes by K-means clustering and distribution of subtypes by biopsy site. A, Heatmap showing K-means cluster and the expression of key marker genes (AXL and MITF) and cell type scores generated by xCell. B, Distribution of K-means subgroups across biopsy sites. C, OS by K-means subgroup and treatment arm. Bini, binimetinib; Vemu, vemurafenib.

Supplemental data file contains Table S1, S2 and Figures S1-S7

PFS and OS for encorafenib plus binimetinib or encorafenib vs. vemurafenib by (A and B) ERBB2 expression level and (C and D) PI3K pathway mutation status. Bini, binimetinib; BM, biomarker; Enco, encorafenib; Vemu, vemurafenib.