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International Journal of Radiation Oncology*Biology*Physics

Elsevier BV

Preprints posted in the last 7 days, ranked by how well they match International Journal of Radiation Oncology*Biology*Physics's content profile, based on 21 papers previously published here. The average preprint has a 0.04% match score for this journal, so anything above that is already an above-average fit.

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Tumor Biology and Patterns of Recurrence in High-Grade Glioma: Implications for Radiation Target Delineation

Barve, R.; Gowda, D.; Illiayaraja, K. J.

2026-04-25 oncology 10.64898/2026.04.23.26351633 medRxiv
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Abstract: Purpose: Recurrence in high grade glioma (HGG) predominantly occurs within the high dose radiation field, raising the question of whether treatment failure reflects limitations in radiation target delineation or is driven by intrinsic tumor biology. This study evaluated recurrence patterns following standard chemoradiotherapy and their treatment implications. Material and Methods: This retrospective single center study included 41 patients with histologically confirmed HGG treated with surgery followed by radiotherapy with concurrent and adjuvant temozolomide (TMZ). Patients were followed through August 2018; those with recurrence were included in the analysis. Recurrence patterns were classified based on their spatial relationship to the 60 Gy isodose line as central, infield, marginal, or distant. Survival outcomes were estimated using the Kaplan-Meier method and compared using the log rank test. Results: The most common pattern of recurrence was central (15 patients, 36.5%), followed by infield (11, 26.8%), distant (6, 14.6%), marginal (5, 12.1%), and multicentric (4, 9.8%). Central and in field recurrences (local failures) accounted for 26 patients (63%). Median overall survival (OS) was 27 months, and median progression-free survival (PFS) was 12 months. Survival differed significantly by recurrence pattern (log-rank p = 0.018), with marginal recurrence associated with more favorable outcomes. Conclusion: The predominance of central and infield recurrences within the high-dose region suggests that treatment failure in HGG is not solely explained by inadequate target delineation and may also be driven, in part, by intrinsic tumor biology, including radioresistant subpopulations and tumor heterogeneity. Future strategies may benefit from incorporating biologically guided approaches alongside optimization of radiation treatment parameters.

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Generalizable Deep Learning Framework for Radiotherapy Dose Prediction Across Cancer Sites, Prescriptions and Treatment Modalities

Chang, H.-h.; Cardan, R.; Nedunoori, R.; Fiveash, J.; Popple, R.; Bodduluri, S.; Stanley, D. N.; Harms, J.; Cardenas, C.

2026-04-22 radiology and imaging 10.64898/2026.04.17.26350770 medRxiv
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Optimizing radiotherapy dose distributions remain a resource-intensive bottleneck. Existing AI-based dose prediction methods often have limited generalizability because they rely on small, heterogeneous datasets. We present nnDoseNetv2, an auto-configured, end-to-end framework for dose prediction across diverse disease sites (head and neck, prostate, breast, and lung), prescription levels (1.5-84 Gy), and treatment modalities (IMRT, VMAT, and 3D-CRT). By integrating machine-specific beam geometry with 3D structural information, the framework is designed to generalize across varied clinical scenarios. A single multi-site model was trained on 1,000 clinical plans. On sites seen during training, performance was comparable to specialized site-specific models. On unseen sites (liver and whole brain), the model outperformed site-specific models, with mean absolute errors of 2.46% and 6.97% of prescription, respectively. These results suggest that geometric awareness can bridge disparate anatomical domains while eliminating the need for site-specific model maintenance, providing a scalable and high-fidelity approach for personalized radiotherapy planning.

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ClonoScreen3D-CRISPRi Uncovers Genetic Modifiers of Radiation Response in Glioblastoma

Lee, S.; Husmann, A.; Li, J.; Li, C. Z.; Modi, S.; Ahmad, S.; Mackay, S.; Paul, A.; Jackson, M. R.; Chalmers, A. J.; McCarthy, N.; Gomez-Roman, N. J.; Bello, E.

2026-04-21 cancer biology 10.64898/2026.04.17.719014 medRxiv
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Background: Glioblastoma (GBM) is the most aggressive primary brain tumor in adults. Radioresistance, partly mediated by glioma stem-like cells, represents a major clinical challenge which could be overcome by the identification of the modulators of radioresistance. Existing CRISPR screens in human GBM models have largely used two-dimensional cultures with short-term viability readouts, failing to capture the long-term clonogenic behaviour underlying tumour recurrence after radiotherapy. Method: We developed ClonoScreen3D-CRISPRi, combining CRISPRi-mediated gene knockdown with three-dimensional clonogenic survival assays. Two GBM cell lines (G7 and GBML20), differing in MGMT promoter methylation status, were engineered to express the KRAB-dCas9 editor. Nine candidate radiosensitivity modifiers, selected through transcriptomic analysis, pharmacological studies, and literature review, were examined in both lines. Target validation was performed using full radiation dose-response assays and a pharmacological inhibitor. Results: The majority of candidate genes significantly altered survival fraction following irradiation in both cell lines. Knockdown of NFKB2, RELB, and CDK9 produced the most potent radiosensitization, with sensitizer enhancement ratios of 1.39-1.70 in validation studies, exceeding those of established radiosensitizers including PARP and ATM inhibitors. Notably, knockdown of these genes induced no significant cytotoxicity in the absence of radiation. Pharmacological validation using an IKK inhibitor confirmed these findings, implicating non-canonical NF-{kappa}{beta} signalling and CDK9-dependent transcriptional elongation as critical adaptive mechanisms in GBM radioresistance. Conclusions: ClonoScreen3D-CRISPRi is a scalable, physiologically relevant platform for identifying genetic modifiers of radioresistance. The non-canonical NF-{kappa}{beta} pathway and CDK9 represent promising radiosensitizing targets, and larger screens could enable systematic prioritisation of candidates for clinical translation.

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Evaluation of Neuronal Activation Thresholds for Low-Frequency Electromagnetic Exposure Using Morphologically Realistic Neuron Models

Gazquez, J.; Camacho Cadena, C.; He, W.; Yamada, E.; Altekoester, C.; Soyka, F.; Laakso, I.; Hirata, A.; Joseph, W.; Tarnaud, T.; Tanghe, E.

2026-04-21 neuroscience 10.64898/2026.04.17.719188 medRxiv
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International guidelines for low-frequency electromagnetic field exposure (LF EMF) are primarily intended to prevent substantiated adverse effects. In the frameworks, limits on internal electric fields are linked to external exposure levels through computational dosimetry. However, the relationship between internal electric fields and these adverse effects remains incompletely understood. In particular, current approaches often overlook the morphological complexity and diversity of cortical neurons, which may limit the realism of neuronal activation estimates used to support these assessments. This study evaluates LF EMF-induced neural activation using 25 morphologically realistic neuron models spanning all cortical layers, embedded within 11 detailed human head models. The internal electric fields were simulated for uniform magnetic field exposures (100 Hz-100 kHz) along the three anatomical directions, and excitation thresholds were computed using a multi-scale framework combining voxel-based dosimetry with biophysical neuron simulations. A real-world exposure scenario involving a child near an acousto-magnetic article-surveillance deactivator was also analyzed. Thresholds varied across cell type, morphology, cortical location, subject anatomy, frequency, and exposure direction, with L2/3 pyramidal, L4 basket, and L5 thick-tufted pyramidal cells showing the lowest thresholds. Despite this variability, all simulated thresholds were conservative with respect to the basic restrictions and dosimetric reference limits set by IEEE ICES and ICNIRP. The smallest margin occurred at 100 kHz, where the threshold remained a factor of 2.8 above the corresponding limit. These findings indicate that current LF EMF exposure limits remain conservative when evaluated using highly detailed, morphology-based CNS activation models.

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Comparison studies between Cesium-137 and X-ray irradiators in epithelial injury using in vitro and in vivo models

Lakha, R.; Orzechowska-Licari, E. J.; Kesavan, S.; Wu, Z. J.; Rotoli, M.; Giarrizzo, M.; Yang, V. W.; Bialkowska, A. B.

2026-04-21 cell biology 10.64898/2026.04.17.719248 medRxiv
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Radiation-induced intestinal injury is a widely used model for studying mechanisms regulating tissue injury and regeneration. Traditionally, Cesium (137Cs) radiation has been used in research applications, but over the past decade, X-ray irradiation has become increasingly favored due to its improved safety and non-radioactive profile. Since each type of radiation has distinct physical characteristics that drive its performance, we sought to systematically compare the effects of the X-ray and 137Cs irradiators on intestinal epithelial injury and regeneration. Using established in vitro models, including colorectal cancer cell lines such as HCT116, RKO, and DLD-1, and mouse intestinal organoids, alongside an in vivo model, Bmi1-CreER;Rosa26eYFP, we evaluated differences in transcriptional, protein, and histopathological responses to irradiation. Our results demonstrate that X-ray produced intestinal injury and regenerative responses comparable to those induced by 137Cs, supporting its reliability as an alternative modality for studying intestinal radiation.

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CT-Based Deep Foundation Model for Predicting Immune Checkpoint Inhibitor-Induced Pneumonitis Risk in Lung Cancer

Muneer, A.; Showkatian, E.; Kitsel, Y.; Saad, M. B.; Sujit, S. J.; Soto, F.; Shroff, G. S.; Faiz, S. A.; Ghanbar, M. I.; Ismail, S. M.; Vokes, N. I.; Cascone, T.; Le, X.; Zhang, J.; Byers, L. A.; Jaffray, D.; Chang, J. Y.; Liao, Z.; Naing, A.; Gibbons, D. L.; Vaporciyan, A. A.; Heymach, J. V.; Suresh, K. S.; Altan, M.; Sheshadri, A.; Wu, J.

2026-04-23 oncology 10.64898/2026.04.21.26351428 medRxiv
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Background: Immune checkpoint inhibitors (ICIs) have revolutionized cancer therapy but can cause serious immune-related adverse events (irAEs), with pneumonitis (ICI-P) being among the most severe. Early identification of high-risk patients before ICI initiation is critical for closer monitoring, timely intervention, and improved outcomes. Purpose: To develop and validate a deep learning foundation model to predict ICI-P from baseline CT scans in patients with lung cancer. Methods: We designed the Checkpoint-Inhibitor Pneumonitis Hazard EstimatoR (CIPHER), a deep learning foundation model that combines contrastive learning with a transformer-based masked autoencoder to predict ICI-P from baseline CT scans in patients with lung cancer. Using self-supervised learning, CIPHER was pre-trained on 590,284 CT slices from 2,500 non-small cell lung cancer (NSCLC) patients to capture heterogeneous lung parenchymal patterns. After pre-training, the model was fine-tuned on an internal NSCLC cohort for ICI-P risk prediction, using images from 254 patients for model development and 93 patients for internal validation. We compared CIPHER with classical radiomic models and further evaluated it on an external NSCLC cohort of 116 patients. Results: In the internal immunotherapy cohort, CIPHER consistently distinguished patients at elevated risk of ICI-P from those without the event, with AUCs ranging from 0.77 to 0.85. In head-to-head benchmarking, CIPHER achieved an AUC of 0.83, outperforming the radiomic models. In the external validation cohort, CIPHER maintained strong performance (AUC = 0.83; balanced accuracy = 81.7%), exceeding the radiomic models (DeLong p = 0.0318) and demonstrating higher specificity without sacrificing sensitivity. By contrast, the radiomic model showed high sensitivity (85.0%) but markedly lower specificity (45.8%). Confusion matrix analysis confirmed the robust classification performance of CIPHER, correctly identifying 80 of 96 non-ICI-P cases and 16 of 20 ICI-P cases. Conclusions: We developed and externally validated CIPHER for predicting future risk of ICI-P from pre-treatment CT scans. With prospective validation, CIPHER may be incorporated into routine patient management to improve outcomes.

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Comparing Gleason Pattern 4 Measurement Approaches on Prostate Biopsy Using Machine Learning: A Proof-of-Principle Study

Buzoianu, M. M.; Yu, R.; Assel, M.; Bozkurt, A.; Aghdam, H.; Fine, S.; Vickers, A.

2026-04-24 oncology 10.64898/2026.04.23.26351615 medRxiv
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Objective: To demonstrate the proof of principle that machine learning (ML) can be used to quantify Gleason Pattern (GP) 4 on digitized biopsy slides using multiple measurement approaches, allowing direct comparison of their prognostic performance. Methods: We assembled a convenience sample of 726 patients with grade group 2-4 prostate cancer on systematic biopsy who underwent radical prostatectomy between 2014 and 2023. Digitized biopsy slides were analyzed using a machine-learning algorithm (PAIGE-AI) to quantify GP4 using multiple measurement approaches, particularly with respect to how gaps between cancer foci (interfocal stroma) were handled. GP4 extent was quantified using linear measurements or a pixel-based area metric. Discrimination of each GP4 quantification approach, along with Grade Group (GG), was assessed for adverse radical prostatectomy pathology and biochemical recurrence. Results: We identified 15 different quantification approaches and observed differences between their discrimination. The highest discrimination was in the pixel-counting method (AUC 0.648). GP4 quantification outperformed GG for predicting adverse pathology (AUC 0.627 vs 0.608). Amount of GP3 was non-predictive once GP4 was known. These findings were consistent for BCR. Conclusions: We were able to measure slides using 15 distinct measurement approaches and replicated prior findings using ML to quantify GP4. Our findings support the use of ML as a research tool to compare different GP4 quantification approaches. We intend to use our method on larger cohorts to determine with which measurement approach best predicts oncologic outcome.

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Phase 1a Evaluation of LP-184 in Recurrent Glioblastoma: Safety, Pharmacokinetics, and Translational Optimization of CNS Exposure

Schreck, K.; Lal, B.; Zhou, J.; Lopez Bertoni, H.; Holdhoff, M.; Ewesudo, R.; Bhatia, K.; Chamberlain, M.; Laterra, J.

2026-04-24 oncology 10.64898/2026.04.21.26351406 medRxiv
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Purpose: Limited CNS bioavailability and pharmacodynamics are obstacles to effective systemic therapies for glioblastoma. One strategy to overcome these challenges is drug combinations enhancing CNS penetration and/or tumor chemosensitivity. LP-184, a synthetic acylfulvene class alkylator, induces DNA damage and inhibits glioblastoma cell viability in pre-clinical models. LP-184 is a prodrug converted to active metabolites by intracellular prostaglandin reductase 1 (PTGR1) that is over-expressed in >70% of glioblastoma. DNA damage induced by LP-184 is MGMT agnostic and reversed by transcription-dependent NER. Patients: LP-184 was evaluated in a Phase 1a study (NCT05933265) in 63 adult patients with advanced malignancies including 16 patients with recurrent glioblastoma. All patients with glioblastoma received prior standard-of-care therapy and most had received 1 or more additional therapies before enrollment. Results: Patients with glioblastoma experienced more frequent transaminitis, Grade 1-2 nausea and a trend towards more frequent and severe thrombocytopenia compared to the non-glioblastoma cohort. Otherwise, overall toxicity profiles were similar. Clinical pharmacokinetic analysis combined with published pre-clinical intra-tumoral bioavailability data (~20% penetration) predicted that LP-184 at the recommended dose for expansion (RDE) would achieve cytotoxic levels if combined with spironolactone, a BBB permeable ERCC3 degrader and TC-NER inhibitor that sensitizes glioblastoma cells to LP-184 3-6-fold. We show that three daily doses of spironolactone deplete orthotopic glioblastoma PDX ERCC3 protein by ~ 80% and increases tumor LP-184 cytotoxicity 2-fold. Conclusions: LP-184 is well tolerated at the RDE, and we establish a clinically translatable scheme for dosing spironolactone in combination with LP-184 for a future Phase 1b clinical trial.

9
Differential effects of BCG-Russia and BCG-TICE on trained immunity: potential implications for bladder cancer immunotherapy

Nauman, R. W.; Greer, P. A.; Craig, A. W.; Cotechini, T.; Siemens, D. R.; Graham, C. H.

2026-04-21 immunology 10.64898/2026.04.17.719184 medRxiv
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In recent years, immunotherapy of patients with higher-risk non-muscle invasive bladder cancer (NMIBC) in North America has relied on the use of the TICE strain of BCG. However, limitations in the supply chain have warranted investigation of the therapeutic benefit of other strains of BCG, such as BCG-Russia. Trained immunity, a form of innate immune memory, is now widely believed to be an important component of the therapeutic benefit of BCG. Therefore, in the present study we compared the effects of BCG-TICE and BCG-Russia on the acquisition of trained immunity and related secondary immune responses. C57BL/6 mice received a single intravenous injection of BCG-Russia or BCG-TICE. Four weeks later, bone marrow was collected for flow cytometric analysis of hematopoietic stem and progenitor cell (HSPC) populations, generation of bone marrow-derived macrophages, functional assessment of trained immunity, and transcriptomic profiling. Compared with BCG-Russia, BCG-TICE elicited stronger levels of trained immunity, characterized by higher production of several proinflammatory cytokines upon secondary activation. BCG promoted the expansion of HSPCs independent of strain. BCG-TICE was linked to upregulation of key inflammation-related genes and enrichment of functionally relevant pathways. The results of this study reveal strain-dependent differences in the ability of BCG to induce innate immune memory and inflammatory pathways that could ultimately determine efficacy of immunotherapy of patients with NMIBC.

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Feature-Based Parametric Response Mapping on Thoracic Computed Tomography for Robust Disease Classification in COPD

Namvar, A.; Shan, B.; Hoff, B.; Labaki, W. W.; Murray, S.; Bell, A. J.; Galban, S.; Kazerooni, E. A.; Martinez, F. J.; Hatt, C. R.; Han, M. K.; Galban, C. J.; Ram, S.

2026-04-27 radiology and imaging 10.64898/2026.04.24.26351675 medRxiv
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Purpose: To develop an interpretable feature-based Deep Parametric Response Mapping (PRMD) method that combines wavelet scattering convolution networks and machine learning to spatially detect and quantify functional small airways disease (fSAD) and emphysema on paired inspiratory-expiratory CT scans, with enhanced noise robustness. Materials and Methods: In this retrospective analysis of prospectively acquired data (2007-2017), we developed and validated a deep learning-based PRM approach using paired CT scans from 8,972 tobacco-exposed COPDGene participants ([&ge;]10 pack-years; mean age 60.1 {+/-} 8.8 years; 46.5% women), including controls with normal spirometry (n = 3,872; controls), PRISm (n = 1,089), GOLD 1-4 COPD (n = 4,011). Data were stratified into training, validation, and testing sets (24:6:70). PRMD extracts translation-invariant image features using a wavelet scattering network and applies a subspace learning classifier to classify voxels as emphysema or non-emphysematous air trapping (fSAD). PRMD was compared with conventional density-based PRM for voxel-wise agreement, correlation with pulmonary function, robustness to noise, and sensitivity to misregistration using Pearson correlation, Bland-Altman analysis, and paired t tests. Results: PRMD achieved 95% voxel-wise agreement with standard PRM (r = 0.98) while demonstrating significantly greater robustness under noise. PRMD showed stronger correlations with FEV1; (emphysema: r = - 0.54; fSAD: r = - 0.51; P < 0.0001) than standard PRM (r = - 0.42 for both; P < 0.0001). Under simulated high-noise conditions, standard PRM overestimated disease by ~15%, whereas PRMD limited error to < 5% (P < 0.001). Conclusion: PRMD provides an interpretable, feature-driven and noise-resilient alternative to traditional PRM for emphysema and fSAD classification, enhancing the reliability of CT-based COPD phenotyping for multi-center studies and low-dose imaging applications.

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Practical Management of Adverse Events Associated with Bispecific Antibodies for the Treatment of Multiple Myeloma: A Qualitative Interview Study

Graham, T. R.; White, M. G.; Blue, B.; Hartley-Brown, M.; Hunter, B. D.; Huynh, C.; Joseph, N.; Keruakous, A.; Pan, D.; Rudolph, P.; Sawhney, R.; Suvannasankha, A.

2026-04-27 oncology 10.64898/2026.04.24.26350878 medRxiv
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PURPOSE: Bispecific antibodies (BsAbs) represent a major advancement in the management of relapsed/refractory multiple myeloma (RRMM), offering high response rates even in heavily pretreated patients. However, their use presents operational, safety, and supportive care complexities that require coordinated care teams, and evolving infrastructure. This manuscript summarizes best practice recommendations for adverse event (AE) management, outpatient operational models, referral pathways, and emerging strategies to optimize long-term tolerability. METHODS: Medlive, A PlatformQ Health Brand, conducted qualitative interviews of academic and community-based clinicians. Discussions focused on BsAb implementation, patient selection and counseling, and AE management. Experts provided recommendations on team-based protocols, transitions of care, and inpatient versus outpatient considerations. RESULTS: Ten hematologists/oncologists (academic n=4; community n=6) described practice patterns, barriers, and perspectives on BsAb use. BsAbs were consistently regarded as highly effective across multiple lines of therapy, particularly for patients without alternatives. Cytokine release syndrome (CRS) was the most common acute toxicity, generally low grade and managed effectively with early tocilizumab, including prophylactic use in outpatient settings. Immune effector cell-associated neurotoxicity syndrome (ICANS) was rare, mild, and best mitigated through early recognition and caregiver support. Infections, largely from BCMA-associated hypogammaglobulinemia, frequently interrupted therapy, necessitating antiviral prophylaxis, pneumocystis jirovecii pneumonia (PJP) prophylaxis, and intravenous immunoglobulin (IVIG). Outpatient step-up dosing is expanding, supported by prophylactic strategies and academic-community collaboration. Timely referral was emphasized to preserving eligibility. Major outpatient challenges included sequencing, infrastructure readiness, and standardized caregiver and staff education. CONCLUSION: Effective community implementation of BsAbs requires multidisciplinary coordination, standardized AE protocols, infection prevention, and infrastructure to support monitoring, referrals, and equitable access. These measures are critical to ensure safe, sustainable integration of bispecific therapies and to optimize patient outcomes.

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Ultra-high field microstructural MRI of living cortical organoids

Nikolaeva, T.; Jakobs, C. E.; Yon, M.; Adolfs, Y.; Singer, R.; Pasterkamp, R. J.; Krug, J. R.; Tax, C. M. W.

2026-04-22 biophysics 10.64898/2026.04.19.719203 medRxiv
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Quantitative microstructural magnetic resonance imaging (MRI) can noninvasively characterize tissue configuration at micrometer scales, but clinical uptake is limited by validation and optimization in human-relevant scenarios. Organoids are powerful human-relevant tissue models, yet translation is hampered by lack of non-destructive, longitudinal microstructural assessment. Bridging these gaps, microstructural MRI of living organoids can accelerate MRI biomarker and organoid development and validation. Here, we address key obstacles to enable organoid microstructural MRI. First, we use a unique 28.2 T MRI system to achieve spatial resolution with adequate signal-to-noise ratio and feasible scan times. Second, we implement flexible acquisitions with fast readouts to expand multivariate experimental capacity. Third, we develop a workflow combining 3D MRI and 3D lightsheet microscopy for cross-modality anatomical comparison beyond 2D. Using this platform, we demonstrate microstructural MRI of cortical organoids with resolutions down to (20 {micro}m)3, revealing anisotropy, heterogeneity, maturation-dependent differences, and temporal changes in cortical organoids. Correlative lightsheet microscopy confirms correspondence to axonal and nuclear architecture. This platform enables live-organoid MRI as a complementary tool to human- and animal imaging for robust microstructural assessment.

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Accessible and Reproducible Renal Cell Carcinoma Research Through Open-Sourcing Data and Annotations

de Boer, S.; Häntze, H.; Ziegelmayer, S.; van Ginneken, B.; Prokop, M.; Bressem, K. K.; Hering, A.

2026-04-23 radiology and imaging 10.64898/2026.04.22.26351451 medRxiv
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Background: Medical imaging, especially computed tomography and magnetic resonance imaging, is essential in clinical care of patients with renal cell carcinoma (RCC). Artificial intelligence (AI) research into computer-aided diagnosis, staging and treatment planning needs curated and annotated datasets. Across literature, The Cancer Genome Atlas (TCGA) datasets are widely used for model training and validation. However, re-annotation is often necessary due to limited access to public annotations, raising entry barriers and hindering comparison with prior work. Methods: We screened 1915 CT scans from three TCGA-RCC databases and employed a segmentation model to annotate kidney lesion. After a meta-data-based exclusion step, we hosted a reader study with all papillary (n=56), chromophobe (n=27) and 200 randomly selected clear cell RCC cases. Two students quality checked and corrected the data as well as annotated tumors and cysts. Uncertain cases were checked by a board-certified radiologist. Results: After data exclusion and quality control a total of 142 annotated CT scans from 101 patients (26 female, 75 male, mean age 56 years) remained. This includes 95 CTs with clear cell RCC, 29 with papillary RCC and 18 with chromophobe RCC. Images and voxel-level annotations of kidneys and lesions are open sourced at https://zenodo.org/records/19630298. Conclusion: By making the annotations open-source, we encourage accessible and reproducible AI research for renal cell carcinoma. We invite other researchers who have previously annotated any of these cohorts to share their annotations.

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Functionalized nanoparticle transforms cold to hot adenoid cystic carcinoma of salivary gland tumour microenvironment in vitro

Chakraborty, R.; Shah, R.; Chien, A.; Akter, M.; Amirkhani, A.; Winn, T.; Shen, C.; Shahbazi, M.-A.; Tukova, A.; Shannon, K.

2026-04-21 cancer biology 10.64898/2026.04.18.719423 medRxiv
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Adenoid cystic carcinoma (ACC) of salivary gland is a "immune-cold" tumour. Annexin A3 (ANXA3) is an apoptotic protein found to be participating in immune cell infiltration in tumour microenvironment (TME) of various cancer cases. Significant low expressions of ANXA3 protein found in adenoid cystic carcinoma. We hypothesized overexpressing ANXA3 transforms ACC "cold" TME to "hot". We cultured UM-HACC-2A and UFH2 spheroids on extracellular matrix and co cultured them with peripheral blood mononuclear cells. We functionalized FDA (The Food and Drug Administration) approved Poly(lactic-co-glycolic acid) PLGA nanoparticles with anti-cMyb antibody and ANXA3 recombinant protein using streptavidin-biotin conjugation. Upon overexpressing ANXA3 in ACC spheroids in immune coculture model using functionalized nanoparticles, significant increase of tumour infiltrating lymphocytes and decrease in the size of the ACC spheroids observed. Apoptotic profiler assay further confirmed significant upregulation of apoptotic proteins, some of them participate in immune infiltration. Overall, this project exhibits promising results showing potential approach to convert ACC into an immune "hot" tumour.

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Metabolomic Profiling of Dried Blood Spots for Breast Cancer Detection: A Multi-Classifier Validation Study in 2,734 Participants

Anctil, N.; Hauguel, P.; Noel, L.-P.

2026-04-27 oncology 10.64898/2026.04.24.26351695 medRxiv
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Background. Breast cancer (BC) remains the most diagnosed malignancy and leading cancer-related cause of mortality in women worldwide. Although blood-based untargeted metabolomics has emerged as a promising modality for detecting early-stage BC, the clinical translation of this approach has been bottlenecked by two unresolved issues: (i) the field has almost exclusively relied on serum or plasma, which require venipuncture and cold-chain logistics, and (ii) machine-learning models reported on such data are frequently validated with protocols that are blind to analytical batch structure, producing optimistically biased performance estimates. Methods. We present a breast cancer detection study based on dried blood spots (DBS), an analytical matrix that enables self-collection and ambient-temperature shipping. A cohort of 2,734 participants (114 biopsy-confirmed BC cases; 2,620 non-cancer controls) was profiled by untargeted LC-MS/MS on a Thermo Scientific Orbitrap IQ-X coupled to a Vanquish UHPLC. A 39-metabolite panel meeting MSI Level 1 identification criteria was pre-specified a priori from the published breast-cancer metabolomics literature, frozen prior to LC-MS acquisition, and applied to the present cohort without any feature selection on the data. Six standard supervised-learning architectures (LASSO, Elastic Net, Linear SVM, PLS-DA, OPLS-DA, XGBoost) were evaluated on this pre-specified panel; OPLS-DA is reported only in the sex-matched subgroup analysis where a single-seed 5-fold stratified protocol permits a directly comparable fit. Per-batch control-median normalization is applied upstream; kNN imputation, log transform, and robust scaling are fit within each training fold. The evaluation battery comprises batch-aware StratifiedGroupKFold CV at single-seed (seed=42) with inter-seed SD quantified across 10 independent seeds, batch-aware nested CV, a 100-seed held-out 20%-batch validation with disjoint-batch isotonic probability calibration (30% calibration partition), PPV/NPV reporting at multiple operating points and three deployment prevalences, subgroup analyses by TNM stage and tumor grade, pathway-ablation sensitivity analysis, and a 1,000-iteration permutation test. Results. Under batch-aware evaluation (StratifiedGroupKFold, single-seed=42), AUC ranged from 0.914 to 0.949 across classifiers, with LASSO achieving 0.928 and XGBoost 0.949; inter-seed SD across 10 seeds was 0.002-0.006. At 95% specificity, LASSO reached 75.4% sensitivity and XGBoost 81.6%. Held-out batch validation (100 seeds) yielded mean AUC 0.912 for Elastic Net and 0.935 for XGBoost, confirming robust generalization. All 39 panel features showed high coefficient stability, and permutation testing on representative classifiers (LASSO, Linear SVM, PLS-DA) yielded p <= 0.001. Subgroup analyses showed weaker detection of stage IIA tumors (AUC 0.87, n=40) compared with stage IIB/IIIA (AUC 0.95), consistent with stronger metabolic signatures in more advanced disease. Bootstrap coefficient consistency of the Elastic Net classifier confirmed that all 39 panel features received a non-zero multivariate weight in >=80% of 100 stratified bootstraps. Conclusions. On this cohort of diagnosed, pre-treatment breast-cancer cases, DBS LC-MS metabolomic profiling delivers classification performance (AUC 0.928 for LASSO and 0.949 for XGBoost under batch-aware GroupKFold CV at single-seed=42; held-out AUC 0.912-0.935) that is robust across classifier families and biological pathways. The DBS matrix is non-radiating, self-collectable by finger-prick, and mailable at ambient temperature. Performance is weaker on stage IIA than on more advanced disease, and prospective validation in an independent asymptomatic screening cohort is required before clinical positioning as a decentralized triage modality.

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Attention-Guided CNN Ensemble for Binary Classification of High-Grade and Low-Grade Serous Ovarian Carcinoma from Histopathological WSI Patches

rani, a.; mishra, s.

2026-04-22 oncology 10.64898/2026.04.21.26351441 medRxiv
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Accurate histopathological differentiation between High-Grade Serous Carcinoma (HGSC) and Low-Grade Serous Carcinoma (LGSC) remains a critical yet challenging aspect of ovarian cancer diagnosis due to their similar morphology and different clinical outcomes. This study presents a deep learning framework that uses custom attention mechanisms, including the Convolutional Block Attention Module (CBAM), Squeeze-and-Excitation (SE) blocks, and a Differential Attention module within five CNN architectures for automated binary classification of ovarian cancer subtypes from H&E WSI patches. Although individual models achieved higher accuracy, the ensemble stacking framework with a shallow MLP meta-learner delivered the best overall performance, with a ROC-AUC of 0.9211, an accuracy of 0.85, and F1-scores of 0.84 and 0.85 across both subtypes. These findings demonstrate that attention-guided feature recalibration combined with ensemble stacking provides robust and clinically interpretable discrimination of ovarian carcinoma subtypes.

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Quantitative Assessment of Dual and Triple Energy Window Scatter Correction in Myocardial Perfusion SPECT with a 4D Phantom

El Bab, M.; Guvenis, A.

2026-04-25 cardiovascular medicine 10.64898/2026.04.17.26351095 medRxiv
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Conflicting evidence on scatter correction (SC) methods plagues quantitative myocardial perfusion SPECT (MPI), hindering standardized clinical protocols. This simulation study, utilizing the SIMIND Monte Carlo program and a highly realistic 4D XCAT phantom, systematically evaluates Dual Energy Window (DEW, with k=0.5) and Triple Energy Window (TEW) SC techniques. We uniquely investigate their performance across various photopeak window widths (2, 4, and 6 keV) and novel overlapped/non overlapped configurations specifically for Tc 99m MPI parameters largely unexplored in realistic cardiac models. Images were reconstructed with OSEM under uncorrected (UC), SC, and combined attenuation and scatter corrected (ACSC) conditions. Quantitative analysis focused on signal to noise ratio (SNR), contrast to noise ratio (CNR), defect contrast, and relative noise to background (RNB). Our findings consistently show ACSC's superior performance in CNR, SNR, and defect contrast, confirming its critical role. Interestingly, SC alone reduced noise but compromised defect contrast relative to UC, highlighting a potential trade-off without attenuation correction. Crucially, this study reveals minimal influence of photopeak window width and overlap configuration on image quality, and no significant difference between DEW and TEW across most metrics. These results provide essential evidence for optimizing quantitative MPI protocols, suggesting that for Tc 99m, the choice between DEW and TEW, and specific window settings, may be less critical than ensuring robust attenuation correction.

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Chinese Herbal Medicine as a complementary therapy for the management of Colorectal Cancer: Study protocol for a Delphi Expert Consensus survey

Ng, C. Y.; Liu, M.; Ai, D.; Yao, L.; Yang, M.; Zhong, L. L.

2026-04-22 oncology 10.64898/2026.04.21.26350990 medRxiv
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IntroductionColorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide, despite advances in conventional oncological therapies. In recent years, various studies have made advances in integrative oncology, such as investigating the use of Chinese Herbal Medicine (CHM) as a complementary therapy alongside conventional oncological therapies to alleviate treatment-related adverse effects, improve quality of life, and potentially enhance therapeutic outcomes. Despite this, clinical practice in this area remains highly heterogeneous, with limited standardized guidelines on key areas of concern such as (1) optimal intervention, (2) recommended stage and duration of intervention, (3) safety considerations, and (4) possible herb-drug interactions. Hence, this study aims to establish expert consensus on the usage of CHM as a complementary therapy in the management of CRC, to support safe, consistent, and evidence-informed clinical practice. Methods and AnalysisWe will employ a modified Delphi technique to achieve consensus amongst a panel of international experts in various fields related to integrative oncology. Prior to the study, a list of questionnaire items was developed based on a systematic review of existing clinical practice guidelines on CRC. An international panel will be invited based on established international profile in integrative oncology research and clinical practice, and by peer referral. Two rounds of Delphi will be conducted using anonymous online questionnaires. Consensus will be considered reached if at least 50% of the panel strongly agree/disagree that an item should be included or excluded while strong consensus will be set at 76%. Items which achieve strong consensus after Round 1 will be removed, before being sent out for Round 2 with a summary of Round 1 responses for a final consensus. Ethics and DisseminationEthics approval has been obtained from the Institutional Review Board of Nanyang Technological University (IRB-2025-1222). Our findings will be disseminated through peer-reviewed publications and conference presentations. Strengths and limitations of this studyO_LIThis study will develop an expert consensus which aims to guide future integration of Chinese Herbal Medicine (CHM) as a complementary therapy into colorectal cancer (CRC) management. C_LIO_LIKey concerns in areas such as determining the (1) optimal intervention, (2) recommended stage and duration of intervention, (3) safety considerations, and (4) possible herb-drug interactions, thereby laying the groundwork for potential future incorporation of CHM into CRC treatment protocols alongside conventional oncology approaches has been identified, thus limiting implementation in clinical practice. C_LIO_LIDesigning a study e-guide, followed by the consensus rounds study online will facilitate participants responses and the dissemination of information from previous rounds. C_LI

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Coated Bacterial Vaccine Platform Overcomes Weak Antigen Immunogenicity: A Functional Approach to GnRH-Based Immunocastration

Harguindeguy, I.; Assandri, M.; Daza Millone, A.; Cavalitto, S.; Serradell, M.; Ortiz, G.

2026-04-22 immunology 10.64898/2026.04.20.719670 medRxiv
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Immunocastration, a non surgical strategy based on active immunization against gonadotropin-releasing hormone (GnRH), effectively suppresses steroidogenesis and spermatogenesis. However, peptide vaccines targeting poorly immunogenic antigens such as GnRH often fail to elicit robust adaptive immune responses, requiring adjuvants or carrier proteins. Previously, we introduced Coated Bacterial Vaccines (CBVs), a platform that uses chemically inactivated Gram-positive bacteria to display recombinant antigens fused to the SlpA carboxy terminal domain (dSLPA) on their surface. This system leverages natural pathogen associated molecular patterns (PAMPs) to enhance immunogenicity without additional adjuvants. In this work, we extended the application of the CBVs platform to enhance the immune response against a poorly immunogenic GnRH-based peptide vaccine. GnRH-CBVs were formulated using inactivated Bacillus subtilis var. natto coated with a recombinant GnRH tandem repeat dSLPA fusion protein and administered to male BALB/c mice. A chitosan-adjuvanted GnRH dSLPA formulation served as a positive control. GnRH-CBVs induced a strong Th2-biased humoral response, characterized by predominant IgG1 levels comparable to those achieved with chitosan. The resulting antibodies effectively neutralized endogenous GnRH, reducing steroidogenesis and spermatogenesis and inducing marked testicular histological alterations. These findings support CBVs as a promising strategy to enhance peptide vaccine immunogenicity for veterinary immunocastration.

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Histology-Derived Signatures Predict Recurrence Risk and Chemotherapy Benefit in Randomized Trials of Early Breast Cancer

Howard, F. M.; Li, A.; Kochanny, S.; Sullivan, M.; Flores, E. M.; Dolezal, J.; Khramtsova, G.; Hassan, S.; Medenwald, R.; Saha, P.; Fan, C.; McCart, L.; Watson, M.; Teras, L. R.; Bodelon, C.; Patel, A. V.; Symmans, W. F.; Partridge, A.; Carey, L.; Olopade, O. I.; Stover, D.; Perou, C.; Yao, K.; Pearson, A. T.; Huo, D.

2026-04-24 oncology 10.64898/2026.04.23.26351499 medRxiv
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Purpose: To test whether histology-derived gene-expression signatures from routine hematoxylin and eosin slides are prognostic for recurrence and predictive of chemotherapy benefit in early breast cancer. Methods: We conducted a multi-cohort study including CALGB 9344 (anthracycline +/- paclitaxel), CALGB 9741 (standard vs dose-dense chemotherapy), a pooled Chicago real-world cohort, and the American Cancer Society (ACS) Cancer Prevention Studies-II and -3. Whole-slide images were processed with a previously described pipeline to generate 61 histology-derived signatures per patient. The primary endpoint was distant recurrence-free interval (DRFI), except in ACS, where breast cancer-specific survival was used. Secondary endpoints include distant recurrence-free survival (DRFS) and overall survival. The most prognostic signature in CALGB 9344, selected by Harrell's C-index, was evaluated in additional cohorts. Signature-treatment interaction was assessed by likelihood-ratio tests. Multivariable Cox models incorporating age, tumor size, nodal status, estrogen/progesterone receptor status, and signature were fit in CALGB 9344 to improve risk stratification. Results: A total of 7,170 patients were included across four cohorts. The top histology-derived signature in CALGB 9344 showed strong prognostic performance for 5-year DRFI (C-index 0.63) and performed well across validation cohorts (C-index 0.60, 0.70, and 0.62 in CALGB 9741, Chicago, and ACS, respectively). The strongest predictive signal for treatment benefit was observed for DRFS. High-risk cases identified by the signature demonstrated greater benefit from taxane in CALGB 9344 (adjusted hazard ratio [aHR] 0.76 for DRFS, 95% CI 0.66-0.88; interaction p=0.028), from dose-dense chemotherapy in CALGB 9741 (aHR 0.69, 95% CI 0.56-0.85; interaction p=0.039), and differential chemotherapy benefit in the Chicago cohort (aHR 0.84, 95% CI 0.59-1.21; interaction p=0.009). Combined clinical-histology models improved risk stratification and identified low-risk groups with a 2%-10% risk of distant recurrence or breast cancer death. Conclusion: Histology-derived signatures from H&E images are broadly prognostic and, unlike clinical factors, may predict chemotherapy benefit.