Citations

Abstract Background: Therapy-induced senescence (TIS), a tumor cell state associated with distinct gene expression patterns and implicated in therapy resistance, may be activated in Multiple Myeloma (MM) patients (pt) by genotoxic chemotherapies, such as high-dose melphalan (HDM). We investigated whether TIS is activated in MM cells following chemotherapy and linked to resistance to T-cell directed therapies. Method: We integrated scRNA-seq data from healthy donors (CNTRL) and MM pts (newly-diagnosed (NDMM), pre/post-CAR-T) bone marrow plasma cells (PCs) using two public datasets (Boiarsky, et al.; Dhodapkar, et al.) and a newly generated pt dataset. Senescence was evaluated using scGSEA with published gene sets (SenUp, SenGA, and SCAPs). For in vitro MM cytotoxicity assay, human H929 MM cells were treated with vehicle (Veh) or HDM (3µM, IC90) for 6h and examined for TIS features. H929VEH or H929HDM were co-cultured with CNTRL T cells with or without teclistamab (Tec, 10 nM) or with day 14 PBMCs from MM pts post-CAR-T (E:T 5:1). CAR+ T cells were high among the day 14 PBMC (median±SD: 93.4±7.2% of CD3+ cells, n=6). Results: scGSEA revealed significantly higher enrichment of SenUp, SenGA, and SCAPs in late-stage MM cells compared to NDMM and CNTRL (p<0.05). Expression of CDKN2A, encoding the senescence marker p16, was also increased in late-stage MM relative to NDMM/CNTRL PCs. Of interest, cells enriched for senescence also exhibited enrichment for myeloid markers (TET2, CEBP family). Notably, in pre-CAR-T, increased baseline senescence or myeloid marker expression showed an inverse association with CAR-T progression-free survival (PFS), suggesting TIS confers resistance to T cell mediated cytotoxicity. This may be due to myeloid plasticity. TIS MM cells generated in vitro, H929HDM, exhibited a distinct morphology characterized by increased cell size and enhanced cytoplasmic granularity. Increased CD14 expression was seen in 4 of the 6 experiments (median, range % increase: 11.2%, 2.5%-21%), consistent with myeloid plasticity; Increased KLRG1 expression was seen in 5 of the 7 experiments (median MFI ratio, range: 3.7, 1.3-471). No significant change was seen in GPNMB expression. Compared to H929VEH, H929HDM had a reduction in killing by CAR-T cells (median±SD: 22.8±32.94% n=6, p=0.016, Wilcoxon paired test). Similarly, H929HDM had a 10.69% decrease in Tec-mediated T-cell killing compared to H929VEH (n=8, p=0.02, Wilcoxon paired test). Conclusions: Late-stage MM cells exhibit transcriptional signatures consistent with TIS, which can be associated with decreased PFS to CAR-T. We report an in vitro model of TIS MM cells for testing of resistance to T cell killing. Based on these findings, a phase II trial (NCT06940297) is underway to test the hypothesis that peri-CAR-T senolytic therapy with dasatinib and quercetin will deepen responses by targeting this resistant TIS MM population. Citation Format: Christoph Schaefers, Angelo Jose Guilatco, Sofia Arbelaez, Gabriel Alvares Borges, Chen Wu, Andre de Menezes Silva Corraes, Malvika Gupta, Zuoyi Shao, Kevin Regan, Rayaan Kamal, Neal I. Sannuli, Ying Li, Taxiarchis Kourelis, Wilson Gonsalves, Melinda Tan, Nadine Abdallah, Yi Lin, Megan Weivoda. Myeloma cells with therapy-induced senescence-like phenotype have increased resistance to killing by T cell directed therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6475.

Abstract Introduction Revascularization to prevent limb loss is not feasible or represents a very high risk in a significant proportion of patients with chronic limb-threatening ischaemia (CLTI). No standard definition currently exists to define this population of patients. The aim of this study was to develop a consensus-based, multidomain definition to improve clinical assessment and reporting of studies in people with ‘no option’ (NO) or ‘poor option’ (PO) CLTI. Methods A modified Delphi process was conducted with 164 specialists from 30 countries. Two iterative survey rounds were used to reach consensus, defined as ≥70% agreement with a score of ≥7 on a nine-point scale. Results Some 164 international vascular specialists participated in the study, averaging 19 years of experience. A multidomain framework including arterial disease anatomy, biology, risk, function, and context (ABRFC) achieved 83% consensus. A ‘desert foot’ was defined as the absence of distal arterial revascularization targets on advanced non-invasive imaging, invasive digital subtraction angiography, and at least one failed endovascular revascularization attempt (81.6% agreement). Inadequate autogenous bypass conduit was defined as the lack of usable autologous vein across all four limbs (85% agreement). Patients were classified as NO for revascularization if they present with ‘desert foot’, prohibitive medical risk, a non-functional limb, or in those patients who refused arterial revascularization. PO revascularization patients combined factors such as severe infection, lack of autologous vein, or treatment non-compliance (72.1% agreement). Conclusion This consensus study established a structured, expert-validated definition of no option or poor option for revascularisation of patients with CLTI. The multidomain ABRFC framework provides a foundation for standardized clinical assessment, trial design, and future guideline development.

Abstract Large Language Models (LLM) are being widely adopted into the medical field for their impressive ability to analyze and summarize large amounts of text data. These models enable clinicians and researchers to extract meaningful insights from complex datasets and may assist with decision making. Here we present our workflows and application of LLM for the interpretation and summarization of clinical data related to CAR-T cell therapy. Using an LLM (Gemini 2.5 pro) in the Google Cloud Computing (GCP) environment, two applications were developed to analyze CAR-T cell therapy clinical data: 1) extracting and summarizing CRS and ICANS event-related data to streamline the compliance team workflow, and 2) identifying features available at time of CAR-T infusion able to classify patients into high- or low-monitoring needs 14 days post CAR-T. Patient data (vitals, labs, hematology notes, and EKGs) were extracted from the electronic medical record (EMR) using Google BigQuery into SQL tables in GCP. For each application, relevant data fields were retrieved, formatted into JSON objects, and embedded in the LLM prompt for context-aware processing. Both applications have undergone iterative prompt engineering after analyzing the LLM output against ground truth data in the EMR. For the application extracting and summarizing CRS and ICANS events, the LLM was optimized on Mayo Clinic Rochester data. When compared to the IEC compliance database, the LLM achieved 100% accuracy and F1 score for CRS events, and 96% accuracy and 82% F1 score for ICANS events. The match rate for CRS and ICANS grades were 83% and 89% respectively. We applied the same LLM to Mayo Clinic Arizona (MCA) and Mayo Clinic Florida (MCF) cases, who document clinical notes and toxicity flowsheet differently, and achieved an accuracy (MCA: 93%, MCF:93%) and F1 score (MCA: 96%, MCF: 96%) for CRS and accuracy (MCA: 81%, MCF:82%) and F1 score (MCA: 76%, MCF: 75%) for ICANS. LLM was able to capture events missed by manual reviews. For most of the discrepancies where compliance team final adjudication is needed, LLM will be updated to flag discrepancies for review by the compliance team. For the application related to the monitoring needs 14 days post CAR-T, the LLM identified 5 categories predictive of high or low monitoring needs post CAR-T infusion (disease status, inflammatory and tumor burden markers, hematologic status, renal function and performance status). Our model achieved a sensitivity of 85.7%, specificity of 23.8%, and F1 score of 65.5% for our first cohort, compared with data extracted by the LLM from the EMR. For our second cohort, with demographics statistically similar to cohort 1 and using the same 5 categories, the LLM achieved a sensitivity of 83.3%, a specificity of 28.6%, and F1 score of 65.4%. Our workflow and applications of LLM’s provide examples and guidance to others interested in applying LLM’s for clinical and research applications. Citation Format: Emmanuel Contreras Guzman, Matthew Jankowski, Andre De Menezes Silva Corraes, Malvika Gupta, Monica L. Shaw, Madiha Iqbal, Talal Hilal, Saurabh Chhabra, Ricardo Daniel Parrondo, Jody K. Mclean, Kim R. Riester, Kayla Joseph, Melinda Tan, Holly Ross, Cleyonia Barnett, Sylvia Carter, Semy Girmay, Rachel Wolan, Milana Ramsey, Christian Downhour, Kristy Morgan, Shae Sibley, Erica Rushing, Lucy Holmes, Allison Burgstahler, Stephen M. Ansell, Hassan Alkhateeb, Matthew Hathcock, Ramona Bruno, Allison C. Rosenthal, Hemant Murthy, Patrick B. Johnston, Jonas Paludo, Yi Lin. Applications of large language models to CAR-T cell therapy clinical data using Google cloud computing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 2740.

Abstract INTRODUCTION: Colorectal cancer (CRC) is the 2nd most fatal cancer in the U.S.; most benefits of CRC screening are from detection of advanced pre-cancerous lesions (APLs). With a goal to improve non-invasive stool test APL sensitivity, we sought novel APL signatures in stool metaproteomes (host- and gut microbiome-derived proteins) among cancer-free controls (CTRL), APL, and CRC patients. Since dysbiosis in gut microbiota is associated with CRC initiation, we also examined the microbial source of differentially expressed proteins (DEPs). METHODS: Mass spectrometry was performed on archival stool supernatants (n=63 patients; 15 CTRL, 32 APL [16 adenomas & 16 sessile serrated lesions], 16 CRC). A sectioning and database-enrichment strategy was applied for peptide-spectrum matching. Microbial and human-derived proteins were searched against the Integrated Gene Catalogue (IGC) and UniProt human reference proteome. DEPs were identified using thresholds of P < 0.05 and fold-change ≥ 1.5. Pathway annotation of human DEPs was performed with the REVIGO webserver, while gut microbial DEPs were functionally categorized using the KEGG Automatic Annotation Server (KAAS). To assess the taxonomic distribution of microbial DEPs, sequences were aligned against the NCBI non-redundant database using BLASTP. RESULTS: Mass spectrometry detected 879 human and 32,514 microbiome-derived proteins. When limiting detection to proteins present in ≥ 75% of patients, only 117 human and 204 microbial proteins remained. There were 17 (4,875), 288 (9,638), and 63 (3,053) unique human (microbial) proteins detected in CTRL, APL, and CRC groups, respectively. When the protein presence cutoff was set at >30% of patients, there were 52 (13 human [11 upregulated, 2 downregulated], 39 microbial [28 upregulated, 11 downregulated]) DEPs detected for the CRC + APL vs CTRL comparison. Some pathways associated with upregulated human DEPs included: inflammatory response, cellular response to iron, and endothelial cell migration. The top upregulated microbial DEPs were derived from the Phocaeicola, Lachnospiraceae, and Oscillospiraceae genera. The top downregulated microbial DEPs belonged to the Bacteroides, Eubacterium, Agathobacter, Coprococcus, and Blautia genera. CONCLUSION: This work highlights the biological diversity and molecular heterogeneity of the stool proteome. We identified several host and microbial protein markers that differentiate APLs and early CRC from controls. These results provide a foundation for future validation studies, which are necessary to determine the clinical utility of these protein biomarkers prior to their integration into a noninvasive stool test. Citation Format: Emmalee J. Northrop-Albrecht, Vinod K. Gupta, William R. Taylor, Jason P. Sinnwell, Doug W. Mahoney, Patrick H. Foote, Kelli N. Burger, Jaeyun Sung, John B. Kisiel, . Comprehensive investigation of stool metaproteomes among patients with precancerous lesions and colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7656.

Abstract Introduction: Clinical staging of multifocal non-small cell lung cancer (NSCLC) is facilitated by comparative genomic analysis of separate tumor nodules, but the role of genome-wide copy number profiling for this purpose is uncertain. Methods: We analyzed single nucleotide variants (SNVs), gene fusions, small copy number variants (gene amplifications and homozygous deletions) (sCNVs), and large-scale copy number variants (lCNVs) in a retrospective cohort of 34 patients with >1 lung cancer nodule tested on a previously validated tumor-only 515-gene next generation sequencing (NGS) panel (MayoComplete Solid Tumor Panel). For patients with <2 shared SNVs, a Bayesian approach was formulated to calculate the probability of shared versus independent events occurring in different tumor nodules in the same patient. The prevalence of specific lCNVs in NSCLC was derived from an independent dataset of 100 NSCLC peers tested by the same panel, and the prevalence of SNVs, fusions, and sCNVs in NSCLC was derived from publicly available data. Alterations unique to different tumor nodules and suspected germline alterations were excluded from the Bayesian analysis. Results: There were 54 total comparisons for 34 patients. Eleven of the patients (32.4%) had >=2 shared SNVs along with one or more shared lCNVs also identified in each patient. Eight patients (23.5%) had no shared SNVs, gene fusions, sCNVs, or lCNVs. Using the Bayesian approach for the remaining fifteen (44.1%) patients with at least one shared alteration (SNVs, sCNVs, and lCNVs), the probability of clonal relatedness ranged from 73% for a shared whole arm or whole chromosome lCNV to >99% for tumors with two or more shared alterations including multiple or complex lCNVs and SNVs. Whole chromosome or whole arm lCNVs were sometimes shared between tumor nodules with different driver SNVs. Conclusions: Incorporating lCNVs into comparative genomic analysis provides additional evidence of clonal relatedness in a subset of multifocal NSCLCs. However, differences in bioinformatics pipelines for calling lCNVs, concerns over the imprecision of genome-wide copy number profiling, and uncertainty regarding the temporal relationship between lCNVs and carcinogenesis (including somatic events possibly related to “field cancerization”) create challenges for integrating lCNVs into comparative genomic analysis with standard clinical workflows for tumor-only NGS on paraffin embedded tissue sections. Our simplified approach mitigates some of the uncertainty introduced by incorporating lCNVs into clonality determination. Citation Format: Claire Teigen, Ying-Chun Lo, Sounak Gupta, Stephanie Smoley, Beth Pitel, Hussam Al Kateb, Gopi Sivasankaran, Benjamin Kipp, Ande Rumilla, Gang Zheng, Kevin Halling, Katherine Geiersbach, . A Bayesian framework for evaluating somatic copy number variants into comparative genomic analysis of multifocal non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 5423.

Abstract Therapeutic resistance limits the efficacy of radiation therapy in many tumors and provides a compelling rationale to develop novel treatments to enhance radiation sensitivity. DNA-dependent protein kinase (DNA-PK) is a major mediator of DNA repair following radiation, and DNA-PK inhibitors are effective radiosensitizers. WNC0901 is a potent DNA-PK inhibitor in both a cell-free kinase assay (IC50 = 0.073 nM) and a cell-based assay (IC50 = 76 nM). WNC0901 has a 30-fold specificity for DNA-PK relative to other PI3K-related kinases. In a broader kinome screen (363 kinases), 1 μM WNC0901 resulted in >25% inhibition of only five other kinases. There is robust inhibition of radiation-induced DNA-PK autophosphorylation (Ser-2056), as analyzed by Western blotting, with maximal effect at 300 nM WNC0901 in A549 (lung carcinoma), U2OS (osteosarcoma), and HT29 (colorectal) cells. The efficacy of WNC0901 as a radiosensitizer was evaluated in clonogenic assays across these same three radioresistant tumor models. Following treatment with graded concentrations of WNC0901 (0-1000 nM) combined with 2.5 Gy radiation, maximal effects were observed at a 300 nM concentration in A549 (88-fold reduction in relative clonogenic survival compared to RT alone, p<0.001), U2OS (5.8-fold decrease, p=0.002), and HT29 (59-fold decrease, p=0.008) In a full radiation clonogenic, the sensitizer enhancement ratio at 10% survival (SER10) was 3.8 (A549), 2.3 (U2OS), and 1.8 (HT29). In vitro metabolism studies have identified demethylated WNC0901 (WNC0901-M) as a major metabolite. Similar to the parent drug, WNC0901-M is a potent DNA-PK inhibitor with maximal radiosensitizing effects of the metabolite observed at 300nM with SER10 of 2.4 (A549), 1.9 (U2OS), and 1.8 (HT29). The in vivo efficacy of 50 mg/kg WNC0901 combined with 8 Gy was evaluated and compared to another DNA-PK inhibitor, 50 mg/kg peposertib, in A549 tumor heterotopic xenografts. Compared to placebo (median time to endpoint 63 days) or RT alone (median 72 days), the combination of WNC0901 and RT significantly delayed tumor regrowth (median 169 days; p=0.002 compared to RT). Interestingly, peposertib + RT was ineffective (median 83 days; p=0.332 compared to RT). In a second study, similarly robust sensitizing effects of WNC0901 was observed in HT29 xenografts (placebo - median 45 days; RT - median 75 days; RT + WNC0901 - median >110 days; p=.03 relative to RT). Together, these findings demonstrate the robust radiosensitizing effects of WNC0901 in radioresistant tumors and provide a rationale for continued development of this drug. Citation Format: Jessica L. Abraham, Ann C. Mladek, Sonia Jain, Shiv K. Gupta, Paul A. Decker, Matthew L. Kosel, Katrina K. Bakken, Brett L. Carlson, Lauren L. Ott, Danielle M. Burgenske, Jeanette E. Eckel-Passow, Wei Zhong, Jann N. Sarkaria. WNC0901 is a novel DNA-PK inhibitor and potent radiosensitizer of otherwise radioresistant solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6608.

Abstract Background: Tarlatamab, a Delta-like ligand (DLL3)/CD3-targeted bispecific T-cell engager (TCE) is FDA approved in patients (pts) with extensive stage small cell lung cancer (ES-SCLC), after progression on frontline chemoimmunotherapy. We aimed to evaluate the immune cell profile in pts who received this therapy in standard-of-care (SOC) practice with progression free survival (PFS) less than and greater than two months (mo). Methods: Patients who received tarlatamab at Mayo Clinic Rochester and consented to immuno phenotyping of blood are included in the present study. Immune phenotyping was performed on whole blood by flow cytometry and analyzed by Kaluza. Data analysis was performed with Microsoft Excel and PRISM. Results: Eighteen patients with median age 64 (range 37-79) were included in the study. 66% of our cohort were women and 83% had present or past history of smoking, with an average of 40 pack years (range 26-60). With a median follow-up of 2 months, the median PFS for the cohort was 1.5 mo (range 0.33-2.76 months). 61% (13/18) of patients had PFS <2mo. 39% (5/18) had PFS>2mo and of which, three patients had partial response with one maintaining stable disease and one patient with mixed response. At baseline (BL), there were no difference in T cell, CD4 or CD8 cell count between patients in the PFS<2mo and PFS>2mo groups. Patients with PFS<2mo had higher exhausted CD8 T cells compared to those in the PFS>2mo group (CD8+PD1+TIGIT+CD57+, PFS<3mo vs >3mo, cells/mL: 7.14±4.28, 1.58±1.37, p=0.009). Additionally, when analyzing the B-cell population, the PFS<2mo group had lower percentage of B cells compared to the group with PFS>2mo at baseline (6.0±7.5, 10.4±14, p=0.02). At day 7, the group with PFS<2mo had lower Treg compared to the group with PFS>2mo (2.88±1.38, 4.60±1.47, p=0.02). Also, the PFS<2mo group had an increase of B cells compared to the group with PFS>2mo at day 7(<2mo vs >2mo: 10.0±14, 4.37±3.07, p=0.04). Finally, the group with PFS>2mo had decrease in total monocytes (mono), classical mono, and immunosuppressive cells (PFS<2mo vs >2mo, Mono: 340±347, 253±106, p=0.04. Classical mono: 305±283, 155±109, p=0.02. CD14+HLA-DRneg: 105.8±96, 12±39, p=0.03) compared to the group with PFS<2mo by day 7. While no changes were seen between BL and day 7 for intermediate mono in PFS<2mo group, PFS>2mo group had decreased post treatment intermediate monocytes (BL vs day 7, cells/mL, intermed mono: 32.5±15,17.7±6.2, p=0.03). Conclusion: In this study investigating the SOC outcomes of tarlatamab, early progression was associated with higher presence of exhausted CD8 T cells, B cells, and immunosuppressive monocytes. Analysis of additional patients will be shared at AACR meeting. Citation Format: Dhauna Karam Prasad, Andre De Menezes Silva Corraes, Malvika Gupta, Audrey Ma, Chen Wu, Zuoyi Shao, Kevin Reagan, Rayaan Kamal, Ashley Potter, Abdullah Al-Ajmi, Syeda Mina, Sykler J. Taylor, Antonious Hazim, Anastasios Dimou, Kaushal Parikh, Mohammed Shanshal, Ailsa Luce, Anna Schwecke, Julian Molina, Aaron Mansfield, Katherine Smith, Lucy Holmes, Haidong Dong, Yi Lin, Konstantinos Leventakos. Immune cell profile changes in patients treated with tarlatamab for extensive stage small cell lung cancer in real world practice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3931.

ABSTRACT Background Rhabdomyosarcoma is the most common soft tissue sarcoma in pediatrics and infants are reported to have inferior outcomes. ARST1431 recommended delayed primary excision (DPE) while discouraging radiation (RT) deviations. This analysis compared outcomes among very young and older patients in this study. Procedures Demographic and tumor characteristics were summarized using frequencies and percentages. Local failure (LF) frequency was summarized by age group, RT, and DPE status. Event‐free survival (EFS) and overall survival (OS) were estimated using the Kaplan–Meier method and compared between age groups using the log‐rank test. Results Of 296 patients, 48 (16.2%) were <24 months: 14 (4.7%) < 12 months, 34 (11.5%) 12–24 months–compared with 248 (83.8%) ≥24 months. DPE was performed in: 7 (50%), <12 months; 9 (26%), 12–24 months; 56 (22%), ≥24 months. RT was given to 9 (64%), 27 (79%), and 195 (79%) of <12, 12–24, and >24 months, respectively. LF in DPE+RT was 8.3% and 6.1%, < 24 months and ≥ 24 months, respectively, compared to 29.3% and 20.5% for RT without DPE. The 4‐year EFS did not vary: 56% (95% CI = 26.5, 86.0), 68% (95% CI = 51.2, 84.1), and 61% (95% CI = 54.2, 68.3) <12, 12–24, and >24 months old, respectively. Conclusions Outcomes in younger children are comparable to older children with local failure more common in those without DPE. Optimization of local control will be important for future studies. Trial Registration Number NCT02567435