Table S2. KRAS mutations in leukemia

Table S3. HRAS mutations in leukemia

PURPOSE:Biology guided radiation therapy (BgRT), a novel treatment approach, integrates real-time positron emission tomography (PET) imaging with external beam delivery to enable tumor-targeted dose modulation. Lung tumors, given their high ¹⁸F-fluorodeoxyglucose (FDG) uptake and low background activity, are considered ideal candidates for BgRT. This study presents the first clinical experience of BgRT in lung cancer, evaluating treatment workflow, plan quality, PET signal characteristics, and delivery timing. METHODS AND MATERIALS:A consecutive cohort of 27 patients with lung tumors was evaluated for BgRT using the RefleXion X1 platform between December 2023 and January 2025. Of these, 14 patients received stereotactic body radiation therapy in 5 or fewer fractions. PET modeling and pretreatment PET evaluation were performed to assess activity concentration and normalized target signal. Key metrics included treatment completion rate, plan quality parameters, temporal trends in FDG signal across fractions, and a timing analysis of treatment delivery encompassing imaging, planning, and delivery workflows. RESULTS:Among the 14 patients treated with BgRT, 12 completed all planned BgRT fractions. Two were transitioned to conventional image guided radiation therapy due to insufficient PET signal and machine interlock, respectively. PET-based metrics demonstrated stable FDG avidity in most patients with gradual declines in activity concentration and normalized target signal that remained within clinically acceptable thresholds. BgRT plans met institutional dosimetric criteria, achieving a median planning target volume V100% = 95.6% (range, 72.2%-97.7%) and appropriate organ sparing. The median beam-on time was 29 minutes (range, 10-48 minutes), and the median total procedure time was 116 min (range, 91-136 min), supporting clinical feasibility. CONCLUSIONS:BgRT using the RefleXion X1 system is clinically feasible, with preliminary indicators of short-term tolerability among evaluable fractions in lung cancer patients. This initial experience demonstrates reliable PET signal acquisition, consistent plan quality, and efficient delivery. These findings support the potential integration of BgRT into routine practice and justify further prospective studies in other disease sites.

Magnesium serves as an essential cofactor for small GTPases, yet its structural role in regulating KRAS conformational dynamics and nucleotide exchange remains poorly understood. Here, we combine hydrogen-deuterium exchange mass spectrometry (HDX-MS), native mass spectrometry, and functional assays to elucidate how Mg2+ stabilizes the KRAS conformational ensemble and constrains transitions between GDP- and GTP-bound states. Depletion of Mg2+ triggers widespread increases in structural dynamics throughout KRAS-spanning the p-loop, α1-helix, switch I, nucleotide-binding region, and distal helices-revealing a global loosening of the protein fold that favors an open, nucleotide exchange-competent state. Mg2+ titration experiments demonstrate that individual structural elements exhibit distinct Mg2+ dependencies: the p-loop and α1-helix recover native dynamics at micromolar concentrations, whereas switch I requires millimolar levels, underscoring its exceptionally high sensitivity to Mg2+ for structural stabilization. KRAS bound to the catalytic domain of exchange factor SOS1 displays an HDX signature closely resembling the Mg2+-free state, indicating that SOS1 promotes nucleotide exchange by transiently perturbing Mg2+ coordination while simultaneously stabilizing switch I. Consistently, the phosphomimetic KRAS S17E variant, which disrupts a critical Mg2+-coordinating residue, exhibits pronounced global destabilization-reinforcing the central importance of Mg2+ in maintaining structural integrity. Taken together, our findings show that Mg2+ acts as a master regulator of KRAS structural dynamics and reveal Mg2+-sensitive hotspots that might represent promising targets for next-generation KRAS therapeutics.

Kinases are pivotal cell signaling regulators and prominent drug targets. Short peptide substrates are widely used in kinase activity assays essential for investigating kinase biology and drug discovery. However, designing substrates with high activity and specificity remains challenging. Here, we present Subtimizer (substrate optimizer), a streamlined computational pipeline for structure-guided kinase peptide substrate design using AlphaFold-Multimer for structure modeling, ProteinMPNN for sequence design, and AlphaFold2-based interface evaluation. Applied to five kinases, four showed substantially improved activity (up to 350%) with designed peptides. Kinetic analyses revealed >2-fold reductions in the Michaelis constant (Km), indicating improved enzyme-substrate affinity. Designed peptides for MET and ROS1 exhibited reciprocal selectivity, with 4-fold and 11-fold preferences for their intended targets, respectively. This study demonstrates AI-driven structure-guided protein design as an effective approach for developing potent and selective kinase substrates, facilitating assay development for drug discovery and functional investigation of the kinome.

Ewing sarcoma is characterized by a chromosomal translocation resulting in the fusion protein EWSR1::FLI1. We utilize endogenous EWSR1::FLI1 target gene reporters in patient-derived cell lines to perform a high-throughput phenotypic screen to identify small molecules that impair the EWSR1::FLI1 transcriptional program. We discovered that inhibitors of cyclin-dependent kinase 8 (CDK8), including a novel pyridyl imidazole, altered transcription of EWSR1::FLI1 target genes and CDK8 co-localized with EWSR1::FLI1 preferentially on single GGAA DNA binding motifs. Using pooled CRISPR screening, biochemical studies, and chromatin profiling, we discovered that CDK8 inhibitors suppressed proliferation of Ewing sarcoma cells through a gain-of-function mechanism by inducing molecular trapping of the CDK8 kinase module and Mediator complex on chromatin. This mechanism has implications for the development of small molecules to target transcription and suggests that impairment of transcriptional regulatory complex dynamics might serve as a vulnerability in cancers in which the dominant oncogenes act as dosage-sensitive transcription factors.

Respiratory motion is a long-standing challenge for lung stereotactic body radiotherapy (SBRT), particularly for centrally located lung tumors where increased toxicity demands more precise motion management during treatment. Current two-dimensional imaging approaches are insufficient for 3D tumor deformable motion tracking. In this study, we developed and evaluated a Surface-derived Three-dimensional (3D) AI-driven Real-time (STAR) imaging system by transforming a surface imaging system into a 3D real-time imaging solution. STAR integrated two key components: (1) prior-model-free spatiotemporal implicit neural representation (PMF-STINR): a machine-learning sub-system for pretreatment dynamic cone-beam CT (CBCT) reconstruction and motion modeling; and (2) surface-to-deformation network (Surf2DefNet): a deep-learning model that correlates intra-treatment body surface images with internal 3D anatomy and motion fields, trained based on the dynamic CBCT and motion model output of PMF-STINR. Specifically, PMF-STINR reconstructs a reference CBCT and solves an eigenvector-based motion model from a pretreatment CBCT, while Surf2DefNet predicts the motion eigen-vector weightings from surface images, enabling it to infer real-time CBCTs and motion vector fields (MVFs) using intra-treatment surface maps acquired later. We evaluated STAR imaging using both a digital extended cardiac torso (XCAT) phantom with regular and irregular motion patterns and ten patient datasets. The relative error (RE), center-of-mass error (COME), 95th percentile Hausdorff distance (HD95), Dice coefficients (DICE), and Pearson correlation coefficient (PCC) metrics between STAR images and the 'GT' were evaluated. For the XCAT phantom and the ten patients, the mean COME values are within 1 mm for all but one patient (1.3 mm). The RE values were consistently low, and the DICE and PCC values exceeded 0.89 in all cases. The HD95 are all within 2 mm except for one patient (2. 78 mm). These results demonstrate that the STAR imaging system can achieve accurate spatiotemporal reconstructions from surface images, providing CBCTs and MVFs for intra-treatment real-time image-guidance, and has the potential to improve safety and efficacy of SBRT for lung cancer.

Table S1. NRAS mutations in leukemia

The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Lung Cancer Screening provide criteria for selecting individuals for screening and offer recommendations for evaluating and managing lung nodules detected during initial and subsequent annual screening. These NCCN Guidelines Insights focus on recent updates to the NCCN Guidelines for Lung Cancer Screening.

Abstract RAS mutations are prevalent in leukemia, including mutations at G12, G13, T58, Q61, K117, and A146. These mutations are often crucial for tumor initiation, maintenance, and recurrence. Although much is known about RAS function in the last 40 years, a substantial knowledge gap remains in understanding the mutation-specific biological activities of RAS in cancer and the approaches needed to target specific RAS mutants effectively. The recent approval of KRASG12C inhibitors, adagrasib and sotorasib, has validated KRAS as a direct therapeutic target and demonstrated the feasibility of selectively targeting specific RAS mutants. Nevertheless, KRASG12C remains the only RAS mutant successfully targeted with FDA-approved inhibitors for cancer treatment in patients, limiting its applicability for other oncogenic RAS mutants, such as G12D, in leukemia. Despite these challenges, new approaches have generated optimism about targeting specific RAS mutations in an allele-dependent manner for cancer therapy, supported by compelling biochemical and structural evidence, which inspires further exploration of RAS allele-specific vulnerabilities. This review will discuss the recent advances and challenges in the development of therapies targeting RAS signaling, highlight emerging therapeutic strategies, and emphasize the importance of allele-specific approaches for leukemia treatment.

PURPOSE:Radiation-induced cardiac dysfunction (RICD) is a competing cause of morbidity and mortality in patients receiving thoracic radiation therapy (RT). Currently, there are no clinically-validated approaches for early detection of RICD at a time point that affords the potential for mitigation. The goal of this study was to evaluate the potential of global longitudinal strain (GLS) derived from standard-of-care echocardiogram (ECHO) for the early detection of RICD and to assess the association between adverse GLS changes and survival in patients receiving thoracic RT. METHODS AND MATERIALS:A retrospective review of changes in GLS was carried out in patients with primary or secondary lung cancer who received standard-of-care thoracic RT with a mean heart dose of ≥5 Gy and had measurable GLS on ECHOs performed before and after RT. Changes in 2-chamber (2C), 3-chamber (3C), and 4-chamber (4C) GLS and peak average GLS after RT (relative to pre-RT baseline) were quantified. Survival probabilities were estimated in patients with normal versus abnormal GLS. RESULTS:Thirty-eight patients had measurable GLS before and after RT. Abnormal GLS (defined as <18% or >15% relative decline in GLS after RT from a normal baseline value) was present in 31.6% of patients before RT and 57.9% of patients after RT (P = .012). On paired comparisons, the absolute median reduction (IQR) in 2-chamber, 3-chamber, 4-chamber, and average GLS after RT relative to pre-RT baseline was 1.90 (4.43), 3.00 (3.83), 2.50 (3.63), and 2.25 (3.53), respectively, all P < .001. No statistically significant change in left ventricular ejection fraction was noted after RT. Patients with abnormal GLS after RT had significantly worse survival than those with normal GLS on univariable analysis (P = .049). Despite the small sample size of the study, the survival detriment in patients with abnormal GLS after RT strongly trended toward significance on multivariable analysis (P = .063). CONCLUSIONS:Adverse changes in GLS are detectable on standard-of-care ECHOs and precede significant changes in left ventricular ejection fraction in this cohort of high-risk patients with primary and secondary lung cancer receiving thoracic RT. Thus, ECHO-derived GLS has the potential to serve as an early and noninvasive marker of RICD in this patient population and may enable early adoption of GLS-guided cardioprotective therapy, which has been shown to mitigate cardiac dysfunction in patients with cancer receiving cardiotoxic treatments.

Background/Objectives: This study aims to present a structured clinical workflow for offline adaptive Biology-guided Radiotherapy (BgRT) using the RefleXion X1 PET-linac system, addressing challenges introduced by inter-treatment anatomical and biological changes. Methods: We propose a decision tree offline adaptation framework based on real-time assessments of Activity Concentration (AC), Normalized Target Signal (NTS), and bounded dose-volume histogram (bDVH%) metrics. Three offline strategies were developed: (1) preemptive adaptation for minor changes, (2) partial re-simulation for moderate changes, and (3) full re-simulation for major anatomical or metabolic alterations. Two clinical cases demonstrating strategies 1 and 2 are presented. Results: The preemptive adaptation strategy was applied in a case with early tumor shrinkage, maintaining delivery parameters within acceptable limits while updating contours and dose distribution. In the partial re-Simulation case, significant changes in PET signal necessitated a same-day PET functional modeling session and plan re-optimization, effectively restoring safe deliverability. Both cases showed reduced target volumes and improved OAR sparing without additional patient visits or tracer injections. Conclusions: Offline adaptive workflows for BgRT provide practical solutions to address inter-fractional changes in tumor structure and function. These strategies can help maintain the safety and accuracy of BgRT delivery and support clinical adoption of PET-guided radiotherapy, paving the way for future online adaptive capabilities.

PURPOSE:To evaluate the feasibility of translating clinical lung stereotactic ablative radiotherapy (SAbR) templates from Ethos1.1 to Ethos2.0, leveraging new features to facilitate dose fall-off and automate patient-specific beam arrangement. This study aims to streamline planning processes and support broader adoption of online adaptive radiotherapy (ART) for lung SAbR. METHODS:We selected fifteen patients previously treated with adaptive lung SAbR using the Ethos1.1 system, each receiving 40-60 Gy in 5 fractions. Plans were reoptimized in Ethos2.0 using identical parameters (rIMRT) to their clinical counterpart. To evaluate new integrated features, we utilized high-fidelity (HF) mode with and without automatic treatment geometry selection (HF-cIMRT, HF-aIMRT/VMAT). These strategies were compared to assess the impact of Ethos2.0's new features on plan quality and efficiency using RTOG-based metrics and enhanced plan deliverability analysis. Statistical significance was assessed using paired Student's t-tests (α = 0.05). RESULTS:All plans reoptimized in Ethos2.0 demonstrated acceptable plan quality. No statistically significant differences in maximum organ-at-risk doses were observed between evaluated strategies and the clinical plan. For complex cases, human-selected beam geometry proved superior to automated geometry. HF-enabled plans significantly reduced total monitor units, with HF-aVMAT, HF-cIMRT, and HF-aIMRT reporting 3142.4 ± 997.4 (p < 0.001), 3401.8 ± 516.1 (p < 0.001), and 3225.6 ± 484.2 (p < 0.001) compared to clinical 5424.9 ± 1353.4. A trade-off was observed in conformity index, which was 1.06 ± 0.08 (p = 0.006), 1.05 ± 0.06 (p = 0.003), and 1.03 ± 0.05 (p = 0.05) for HF-aIMRT, HF-cIMRT, and HF-aVMAT plans compared to clinical 1.01 ± 0.03. CONCLUSION:Lung SAbR planning strategies can be effectively transitioned from Ethos1.1 to Ethos2.0, improving workflow efficiency with high-fidelity mode and minor adjustments. Automated beam geometry tools enhance planner efficiency for both IMRT and VMAT. To address increased ART workload and staffing demands, leveraging integrated automation tools is essential. The planning strategies presented in this study are straightforward and reproducible for ART-enabled clinics.

This issue highlights the development of a first-in-class small-molecule covalent KRASG12C inhibitor, BBO-8520, which targets both the active (ON) and inactive (OFF) states of KRAS. This dual-state targeting offers a significant opportunity to overcome the resistance mechanisms that have limited the efficacy of first-generation KRAS inhibitors and addresses critical challenges in KRAS-targeted therapy. See related article by Maciag et al., p. 578.

We describe a case of a 69-year-old gentleman with a biopsy-proven non-small cell lung cancer (NSCLC) who was treated with the SCINTIX biology-guided radiotherapy (BgRT). In this report, we focus on the development of our institutional clinical workflow for BgRT to ensure a safe and seamless process. This entails the initial import of diagnostic PET/CT with fluorodeoxyglucose-avid lesion(s), 4D CT simulation, contouring including the biology tracking zone, a patient modeling session for planning PET, and radiation treatment (RT). BgRT is a promising technology that has the potential to allow functional adaptation of RT. In our patient with NSCLC who was treated with 5-fraction BgRT, we were able to achieve the threshold for activity concentration and a sufficiently normalized tumor signal. Furthermore, the time analyses of treatment steps demonstrated an efficient workflow.

A woman in her early 80s with a history of smoking, limited scleroderma, interstitial lung disease (ILD) and pulmonary arterial hypertension developed a right suprahilar mass, avid on positron emission tomography (PET) scan. A biopsy was not performed due to the high risk of complications and the high positive predictive value of malignancy. She was staged as IA3: cT1c N0 M0 and recommended for empiric treatment with stereotactic ablative body radiotherapy (SABR). To manage the risk of treatment-related toxicity due to ILD and the tumour's central location, an adaptive personalised ultra-fractionated stereotactic adaptive radiotherapy (PULSAR) approach was selected, with treatments administered every 3 weeks. A plan for 4000 cGy in 5 fractions was devised, but with each successive fraction, the tumour shrank significantly, resulting in a complete radiographic response and cessation of treatment after 4 fractions. PULSAR may offer a safer approach for managing high-risk lung cancer patients undergoing SABR, but it also introduces unique challenges, such as the potential for complete radiographic response or progression during treatment.

PURPOSE:We investigated the efficacy and toxicity of thoracic radiation therapy (RT) plus concurrent and consolidation carboplatin with either solvent-based paclitaxel (sb-paclitaxel) or solvent-free nanoparticle albumin-bound paclitaxel (nab-paclitaxel). METHODS AND MATERIALS:This multicenter phase 1/2 randomized trial included patients with inoperable stage IIIA/B nonsmall cell lung cancer (AJCC 7) and an Eastern Cooperative Oncology Group performance status of 0-1. In phase 1, 6 patients received weekly nab-paclitaxel (50 mg/m²) and carboplatin (AUC 2) with concurrent thoracic RT (60 Gy in 30 fractions), followed by nab-paclitaxel (100 mg/m²) on days 1, 8, and 15 and carboplatin (AUC 6) on day 1 for two 21-day cycles. In phase 2, 92 patients were randomly assigned to weekly sb-paclitaxel (50 mg/m²) or nab-paclitaxel (40 mg/m²) with concurrent RT, followed by consolidation therapy with sb-paclitaxel or nab-paclitaxel and carboplatin for 2 cycles. RESULTS:Two phase 1 patients had dose-limiting toxicities, setting the phase 2 nab-paclitaxel dose at 40 mg/m². For the phase 2 cohort, 2-year overall survival was 67% for sb-paclitaxel and 56% for nab-paclitaxel (P = .10), with progression-free survival of 44% and 27%, respectively (P = .14). Fewer patients completed consolidation with nab-paclitaxel (26%) versus sb-paclitaxel (58%) (P = .005). Grade 3 and higher adverse events were more frequent with nab-paclitaxel (56%) than with sb-paclitaxel (30%) (P = .029). CONCLUSIONS:Nab-paclitaxel was associated with higher toxicity and numerically lower efficacy than sb-paclitaxel when used with thoracic radiation in locally advanced nonsmall cell lung cancer.

The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Lung Cancer Screening provide criteria for selecting individuals for screening and offer recommendations for evaluating and managing lung nodules detected during initial and subsequent annual screening. These NCCN Guidelines Insights focus on recent updates to the NCCN Guidelines for Lung Cancer Screening.

Doxorubicin (Dox) has been a mainstay in breast cancer treatment for over three decades, but its therapeutic efficacy is often compromised by drug-induced senescence, leading to therapeutic failure. Thus, this underscores the need for innovative therapeutic strategies in breast cancer therapy. To address this challenge, we have identified DCR2, a cell membrane marker of senescent cells, and developed DCR2-targeted ultrasound nanobubbles to counteract Dox-induced senescence in breast cancer. The results showed that DCR2-targeted nanobubbles exhibited a robust ultrasound signal around senescent breast cancer cells and can encapsulate verteporfin (Ver), a phagocytosis inhibitor, to suppress Dox-induced senescence and inhibit breast tumor growth. Notably, using two breast tumor models in MMTV-PyVT and C57BL/6 mice, we showed that DCR2-targeted ultrasound nanobubbles can modulate tumor immune microenvironment and reverse senescence-induced polarization of M2 tumor-associated macrophages. The tumor growth was markedly suppressed by the combined treatment of Dox and Ver-loaded DCR2-targeted nanobubbles. In summary, this study presents a promising approach to overcoming chemotherapy resistance using ultrasound nanobubbles, providing potential improvements in breast cancer treatment outcomes.