Citations

Abstract Objectives Per National Comprehensive Cancer Network guidelines for acute myeloid leukemia (AML), bone marrow (BM) evaluation is recommended after starting induction chemotherapy at 14 to 21 days (mid-induction) and 30 to 35 days (postinduction). Timely assessment of residual morphologic and molecular disease is challenging at these time points, given the low cellularity, the lack of CD34 or CD117 expression by blasts in most NPM1-mutated (NPM1mut) AML, and the longer turnaround time for molecular testing. Methods NPM1 mut AML undergoing BM evaluation at mid- and postinduction with concurrent flow cytometry and NPM1 real-time polymerase chain reaction or next-generation sequencing was evaluated. Different cell types positive by NPM1 immunohistochemistry (IHC) were enumerated, and the results were compared with flow cytometry and molecular findings. Results NPM1 IHC demonstrated a sensitivity of 78% and 41% for detecting residual mutation at mid- and postinduction, respectively, with a positive predictive value ranging from 88% to 100%. Of 16 IHC-negative cases, 3 had no residual NPM1 mutation, 12 had very low-level mutation at a variant allele frequency of less than or equal to 21 transcripts, and only 1 had a high-level mutation in a markedly hypocellular BM. Of 24 IHC-positive cases, 22 had residual NPM1 mutation, and 2 showed false-positive staining in only a single cell with no residual NPM1 mutation. The level of IHC staining was mostly proportional to the level of residual mutation. Conclusions Mutation-specific NPM1 IHC is a valuable tool for a rapid assessment of residual morphologic and molecular disease in mid- and postinduction NPM1mut AML.

Introduction Asymptomatic individuals with negative Interferon-γ release assay (IGRA) and tuberculin skin test (TST) results are often labeled as tuberculosis-unexposed individuals. We hypothesize that flow cytometric (FC) detection of antigen-stimulated T-cells in peripheral blood can differentiate IGRA(-)/TST(-) individuals with and without prior potential M. tuberculosis (Mtb) exposure. Methods We used FC multiparameter profiling of T-cell activation markers in TST/IGRA-negative individuals at risk for Mtb exposure and in unexposed controls. Results We studied 54 IGRA(-)/TST(-) subjects, including 27 individuals at risk for prior Mtb exposure. While quantitative IGRA results were negative in all patients, FC profiling of CD3/CD4 + IFN-γ + HLA-DR + T-cells after stimulation with a pool of Mtb-specific region of difference-1 (RD1) peptides, mycobacterial (PPD and MTB300), or Candida antigens, statistically differentiated between unexposed and potentially exposed individuals (P<0.05). ROC analysis showed PPD and RD1 peptides responses had AUCs >0.7 (sensitivity of 55.5–74% and specificity of 66.6–85.1%). The presence of a polyfunctional RD1-reactive CD3/CD8 + IFN-γ + TNF-α + T-cell subset also significantly differentiated these groups (AUC 0.66). Other T-cell markers demonstrated no significant differences. Conclusions FC detection of antigen-specific IFN-γ + HLA-DR + CD4+T-cells and IFN-γ + TNF-α + CD8 + T-cells can differentiate IGRA(-)/TST(-) individuals at risk of Mtb exposure from unexposed controls. Further validation is needed to determine whether this immunoprofiling approach can improve detection of Mtb infections and identification of unexposed individuals for future biomarker studies and vaccine trails.

COASY-related disorders (CRDs) are a spectrum of autosomal recessive conditions caused by the dysfunction of CoA synthase, an enzyme responsible for the final steps of CoA synthesis. Clinical manifestations of CRDs are highly variable, ranging from perinatal lethal pontocerebellar hypoplasia to childhood-onset neurodegenerative brain iron accumulation, which is often recognized after clinical regression. Recent reports have described a few individuals with CRD who screened positive for carnitine palmitoyltransferase-I deficiency by newborn screening (NBS). However, heterogeneous clinical presentations, conflicting biochemical/molecular sequencing of CPT1A, and a lack of metabolic characterization have led to lengthy, costly diagnostic journeys. To address some of these aspects, this investigation retrospectively evaluated NBS acylcarnitine patterns in five CRD cases using Collaborative Laboratory Integrated Reports (CLIR). A total of 25 metabolites/ratios were identified to deviate significantly from reference ranges and were primarily composed of elevated free carnitine and reduced long-chain acylcarnitine levels. While low acylcarnitine concentrations are often not reported due to a lack of lower reference cutoffs, ratios involving these metabolites relative to short-chain acylcarnitines could aid in identifying CRD cases via NBS. When comparing this pattern to CPT-Ia cases, we confirmed a nearly identical acylcarnitine pattern between these, and thus support the need to consider CRD in cases with NBS results suggestive of CPT-Ia. This study is the first case series to characterize NBS patterns in patients with CRD and highlights the unique opportunity for early detection, particularly in cases that are neonatally asymptomatic and have unremarkable confirmatory biochemical results.

Background: Contemporary rotating-hinge total knee arthroplasties (RH-TKAs) have shown reasonable short-term survivorship in smaller series, but concerns remain regarding risks of aseptic and septic failure. The purpose of this study was to assess outcomes of contemporary RH-TKAs in one of the largest series to date. Methods: We retrospectively identified 575 RH-TKAs (60% used for aseptic etiologies and 40% used during reimplantation in 2-stage treatment of periprosthetic joint infection [PJI]) from 2002 to 2021 at a single institution. The mean age was 67 years, 58% were female, and the mean body mass index was 33 kg/m 2 . Sixty-five percent had Anderson Orthopaedic Research Institute (AORI) type-2B or 3 bone loss. Kaplan-Meier survivorship analyses were performed. The mean follow-up was 6 years (range, 2 to 19 years). Results: Survivorship free from any revision was 76% at 5 years and 64% at 10 years. The most common revision indications were PJI (54%) and aseptic loosening (20%). RH-TKA used in the primary setting showed better survivorship compared with RH-TKA used during reimplantation after PJI (79% versus 60% at 10 years). Survivorship free from revision for aseptic loosening was 96% at 5 years and 90% at 10 years. Survivorship free from revision for PJI was 84% at 5 years and 81% at 10 years. Survivorship free from revision for PJI was even lower for RH-TKAs used during reimplantation, 74% at 5 years and 73% at 10 years. RH-TKA used during reimplantation in the treatment of PJI was associated with an increased risk of any revision (HR = 2, p < 0.001). Radiographic analysis of 425 knees that were not revised and had radiographs available for review showed that 6% of femoral components and 8% of tibial components had evidence of loosening at the time of final follow-up. The mean Knee Society Score improved from 33 to 69 at 2 years (p < 0.001). Conclusions: The 10-year survivorship free from aseptic loosening was 90% in this large series of RH-TKAs. This represents one of the best survivorships free from aseptic loosening published to date. Knees with prior PJI had markedly poorer survivorship than knees treated for aseptic etiologies, with double the risk of revision. Level of Evidence: Therapeutic Level III . See Instructions for Authors for a complete description of levels of evidence.

Objective Immunohistochemically (IHC) measured transactive response DNA‐binding protein 43 (TDP‐43) inclusions are observed in Alzheimer's disease (AD) and are associated with medial temporal lobe atrophy. Accumulation of cryptic exons occurs in AD in response to TDP‐43 pathology. We aimed to assess relationships between IHC and biochemically measured insoluble TDP‐43 and cryptic exons and assess associations with hippocampal and amygdala volume loss and atrophy rates on magnetic resonance imaging (MRI). Methods Eighty‐one neuropathologically diagnosed AD cases were analyzed. For biochemistry, insoluble TDP‐43 was quantified using a Meso‐scale discovery (MSD) immunoassay. IHC‐TDP burden was quantified with digital histopathology. Cryptic RNAs were assessed via quantitative real‐time polymerase chain reaction (qRT‐PCR). Thirty‐eight cases had serial brain MRI. Hippocampal and amygdala volumes were calculated using FreeSurfer. Regression models were used to investigate associations among IHC‐TDP‐43 status/burden, MSD‐TDP status/levels, cryptic RNAs, and hippocampal and amygdala volumes and atrophy rates. Results IHC‐TDP(+) cases exhibited elevated levels of MSD‐TDP and cryptic RNAs ( KCNQ2 , STMN2 , and UNC13A ) and increased MSD‐TDP levels were associated with increased cryptic RNA levels, in the hippocampus and amygdala. IHC‐TDP(+) cases had smaller hippocampal and amygdala volumes compared to IHC‐TDP(−) cases. MSD‐TDP(+) cases had smaller hippocampal volumes and faster amygdala rates of atrophy compared with MSD‐TDP(−) cases. Higher KCNQ2 and UNC13A levels were associated with smaller amygdala volumes. Interpretation MSD‐TDP level is a reliable surrogate for IHC‐based TDP‐43 status. Both TDP‐43 and cryptic RNA levels are associated with reduced medial temporal volumes, suggesting cryptic exons may be playing a role in brain volume loss in AD. ANN NEUROL 2026;100:193–205

Introduction: Calibrated automated thrombogram assay parameters have been shown to assess hypercoagulation state and, therefore, may independently predict posttrauma, symptomatic venous thromboembolism (VTE). Yet, calibrated automated thrombogram lacks high throughput and standardization, limiting diagnostic potential. This study analyzed thrombin generation (TG) profiles in trauma patients using a high-throughput assay, processing up to 10 samples at once, providing batch testing capabilities. We hypothesized that trauma patients who developed VTE would show distinct TG profiles compared with those who did not. Methods: Trauma patients presenting to a Level I Trauma Center had samples collected within 12 hours postinjury prospectively. Follow-up was conducted to 90 days, time to symptomatic VTE diagnosis or death, confirmed via autopsy or imaging. TG profiles were measured from the ST Genesia assay. Data were presented as median (interquartile ranges) or n (%), with the Wilcoxon rank-sum or chi-squared test. Associations between TG parameters and clinical risk factors were assessed using Spearman correlation analysis or the Wilcoxon rank-sum test. Results: Two hundred and fifty-four trauma patients were analyzed [48.5 years (31.0, 62.0), 72.0% male]: 64 patients with VTE (25.2%) to 190 with non-VTE. VTE pts had a median time to VTE of 8 days, with 29 developing deep venous thrombosis, 24 with pulmonary embolism, and 11 with deep venous thrombosis/pulmonary embolism. No significant differences were found in age, sex, or body mass index; significantly more VTE patients underwent surgery and blood transfusions within 24 hours. TG profiles demonstrated accelerated TG in patients who developed VTE compared with non-VTE, with significant differences in peak height ( P = 0.001), time to peak ( P = 0.021), endogenous thrombin potential ( P < 0.001), and velocity index ( P = 0.001). Conclusion: TG profiles using ST Genesia can differentiate trauma patients at high risk of developing VTE. The platform suits clinical labs needing high throughput by providing batch testing capabilities. Study type: Prospective study with less than large effect and no negative criteria. Level of evidence: II.

Abstract Background: Pediatric and AYA sarcomas are rare, biologically heterogeneous tumors with limited noninvasive biomarkers to guide diagnosis, personalized treatment, and disease monitoring. Standard-of-care evaluation relies on invasive biopsies that carry procedural risks and imaging modalities with limited sensitivity for detecting minimal residual disease and distinguishing tumor types. Cell-free DNA (cfDNA) methylation profiling offers a minimally invasive alternative capable of capturing tumor-derived epigenomic alterations and has consistently shown strong clinical utility in adult malignancies. However, genome-wide cfDNA methylation patterns across diverse pediatric and AYA sarcoma subtypes remain poorly defined. Methods: Plasma was collected from 93 pediatric and AYA patients (pediatric &lt;18 years; AYA 15-39 years) representing 27 Ewing sarcoma, 17 rhabdomyosarcoma, 11 liposarcoma, 10 chordoma, 8 synovial sarcoma, 7 chondrosarcoma, 6 osteosarcoma, and 6 fibrosarcoma cases, plus 19 matched healthy donors. cfDNA was isolated from 1 mL plasma, quantified by Qubit, and assessed by Bioanalyzer. Libraries were prepared using the NEBNext EM-seq v2 workflow with PCR cycles scaled to cfDNA input amount. Genome-wide sequencing (15× target depth) was followed by alignment, deduplication, and methylation calling. MultiQC was used to assess depth, duplication rate, conversion efficiency, and CpG coverage. Global methylation summaries were computed, and methylKit was used to generate per-CpG and 1-kb tiling matrices and initiate differential methylation analyses. Results: Ewing sarcoma patients had significantly higher plasma cfDNA concentrations than age- and sex-matched healthy donors (24.4 vs 4.6 ng/mL, p &lt; 0.0001), whereas cfDNA levels for other sarcoma subtypes overlapped with the healthy cohort. Low or undetectable cfDNA concentrations by Qubit were far more common among non-Ewing sarcoma samples (23 of 66) than Ewing sarcoma (1 of 27). All samples achieved sufficient CpG coverage for genome-wide methylation modeling. Global methylation summaries revealed no significant differences in mean β-values across sarcoma subtypes or versus healthy donors. An independent analysis of the Ewing subset identified 299 significant differentially methylated regions (DMRs), supporting the detectability of disease-specific methylation changes. Conclusions: These results demonstrate the feasibility of high-quality cfDNA methylome profiling across a large and diverse pediatric and AYA sarcoma cohort, including in plasma samples with cfDNA concentrations below the limit of detection. While global methylation levels appear broadly similar across subtypes, proof-of-concept DMR analysis in Ewing sarcoma suggests that subtype-specific epigenomic signatures could enable future noninvasive diagnostic tools for pediatric and AYA sarcomas. Citation Format: Lilli J. Greiner, Roman O. Kowalchuk, Jeff Szymanski, Pradeep S. Chauhan, Adam Amundson, Peter J. Schoettler, Wendy Allen-Rhoades, Stephanie F. Polites, Peter S. Rose, Kelly Bailey, Linda McAllister-Lucas, Anita Mahajan, Nadia Laack, Aadel Chaudhuri. Defining genome-wide cfDNA methylation landscapes in pediatric and adolescent and young adult (AYA) bone and soft-tissue sarcomas [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 7885.

Abstract Introduction: Detectable circulating tumor DNA (ctDNA) is associated with inferior outcomes in Ewing sarcoma (ES); however, ctDNA clears in nearly all patients within 2 of the 6 chemotherapy cycles before radiotherapy (RT) or surgery. Given a 3-year EFS of 37% on AEWS 1221 (metastatic) and 5-year EFS of 78% on AEWS 1031 (localized), current ctDNA testing fails to predict most relapses. Extracellular vesicles (EVs) are microscopic particles studied as a biomarker in multiple cancer types. We hope to improve the sensitivity of ctDNA in ES and provide the first application of EVs in ES. Methods: cfDNA was isolated from 1mL plasma, quantified by Qubit, and sequenced as NEBNext Enzymatic Methyl-seq v2 libraries. We performed a systematic unsupervised clustering analysis of 27 ES plasma cfDNA profiles using 4 differentially methylated regions (DMR) subsets (63 strong DMRs, top 30, top 15, and 10 promoter-proximal loci), 3 clustering algorithms (k-means, Ward hierarchical, PAM), and k=2-5 clusters, testing associations with tumor burden and progression. EV analysis involved antibody detection against ES surface markers, including LINGO1, ENPP1, CDH11, and CD99. Concentrations of EVs were determined by standardized and calibrated high-resolution flow cytometry then analyzed with custom-built software to automatically determine and apply gates. Samples were de-identified, randomly coded, and run in triplicates. The senior research technologist responsible for EV analysis was blinded to patient information and clinical data. Results: EV analysis included 36 pre-RT samples from 16 metastatic and 20 localized ES patients from a prospectively maintained biobank, with 27 pre-RT samples in the cfDNA analysis and 19 healthy donor (HD) samples. 35 of 36 patients had chemotherapy before sample collection. cfDNA concentrations were markedly elevated in ES patients compared with HD (24.4 vs 4.6 ng/mL, p&lt;0.0001), and 74% of ES samples exceeded the HD 95th-percentile detectability threshold (7.0 ng/mL). Across clustering configurations, ES cfDNA profiles consistently exhibited reproducible methylation substructure. One configuration (PAM clustering, k = 5, 63 strong DMRs) showed a modest but permutation-supported association with primary tumor size (nominal p ≈ 0.04; empirical p ≈ 0.03-0.04). ES samples had increased EV concentration compared to HD (p&lt;0.001), with AUC 0.988 for distinguishing between ES and HD ENPP1 (p&lt;0.0001). The highest ENPP1 EV values were in patients with large primary tumors (&gt;8 cm vs. ≤ 8cm) and metastatic disease (p=0.066). Conclusions: cfDNA- and EV-based liquid biopsy provide encouraging signals for high ES detectability pre-RT. We also show the first study of EVs as a novel biomarker in ES, which may provide complementary information to ctDNA. Multimodal liquid biopsy in ES may identify candidate patients for systemic or local therapy escalation and facilitate personalized care. Citation Format: Roman O. Kowalchuk, Lilli J. Greiner, Yohan Kim, Rubia Noori, Jeffrey Szymanski, William S. Harmsen, Pradeep S. Chauhan, Adam C. Amundson, Andrea M. McMahon, Peter J. Schoettler, Wendy A. Allen-Rhoades, Stephanie F. Polites, Peter S. Rose, Kelly M. Bailey, Linda M. McAllister-Lucas, Anita Mahajan, Fabrice Lucien-Matteoni, Nadia N. Laack, Aadel A. Chaudhuri. Multimodal liquid biopsy of Ewing sarcoma reveals high sensitivity prior to radiotherapy [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 1149.

Abstract Therapeutic resistance to chemotherapy is frequently the proximate cause of increased tumor burden, cancer treatment failure, and ultimately, patient mortality. The most successful therapy strategy derived from evolutionary practices to date, Adaptive Therapy (AT), leverages the fitness cost of developing therapeutic resistance. AT avoids treating cancer cells with the Maximum Tolerated Dose (MTD) of therapeutic drugs and instead incorporates a series of adaptive dosing schedules. Treatment-sensitive cells are bolstered by modulating or pausing treatment to out-compete and suppress treatment-resistant cell growth. We are evaluating AT for the first time in colorectal cancer, using a syngeneic orthotopic xenograft model. This work represents several key advances: it is the first to longitudinally and non-invasively track sensitive and resistant clones in vivo, to evaluate adaptive therapy in an immunocompetent mouse model, to incorporate multi-drug treatment regimens, and to integrate a targeted therapeutic agent. The dual-bioluminescent sensitive and resistant CT26 cell lines developed for this study allow real-time visualization and quantification of each population throughout tumor progression and treatment. Together, these advances establish a robust and clinically relevant platform for characterizing resistance dynamics and refining adaptive therapy strategies aimed at improving treatment outcomes in colorectal cancer. Citation Format: Harley I. Richker, Bailey Sierra Kane, Gissel Marquez Alcaraz, Ellie Pahl, Ryan Carr, Nagarajan Kannan, Carlo C. Maley. Harnessing clonal dynamics to overcome resistance: An adaptive therapy framework in 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 702.

Abstract Introduction: Ewing sarcoma (EwS) is a FET::ETS family member-driven primary bone cancer demonstrating vast heterogeneity. Between a patient’s primary diagnosis and disease progression, tumor cell state adaptation, microenvironment changes, and the landscape of evolving therapeutic vulnerabilities remain poorly understood. To address these gaps, the Sean Karl Cohort was established in 2025 to conduct the largest single-cell transcriptomic analysis of retrospective paired tumor samples from patients with EwS. Here, we present data from the five analytic teams, and through shared SOPs now expand this cohort to Europe. Methods: Common sample processing SOPs were established to isolate cells from FFPE material from paired patient EwS samples. Single-cell (sc) RNAseq was generated using the GEM-X Flex Gene Expression protocol (10x Genomics). Alex’s Lemonade Stand Foundation (ALSF) Data Lab established a common data processing and integration pipeline with an EwS-specific cell annotation workflow to create a harmonized dataset for downstream analyses. Analytic teams were created to define tumor cell subpopulations and their therapeutic vulnerabilities and to characterize the tumor microenvironment. Data: We demonstrate the feasibility of generating high-quality scRNAseq profiles from retrospective FFPE-preserved EwS tumors. To date, 116 samples have yielded ∼800,000 cells. Integrated analysis reveals reproducible EwS tumor cell states shared across patients with regulatory network analyses nominating candidate therapeutic vulnerabilities. The scale of this international cohort enables saturation analysis for rare cell populations. Paired and longitudinal samples further allow correlation of emergent cell states with therapy resistance and metastatic progression. For example, immune-focused analyses show increases in T cell and macrophage populations in post-therapy samples. A novel, standardized EwS-specific cell annotation workflow has been developed to harmonize analyses and findings. These data will be openly shared with the community through the ALSF Single-cell Pediatric Cancer Atlas Portal. Conclusion: Large-scale international collaborative sample sharing, standardized processing pipelines, and harmonized EwS-specific annotations now enable deep single-cell analyses to characterize tumor heterogeneity in this rare pediatric and adolescent cancer. An in vivo expansion of the Sean Karl Cohort is underway to assess conservation of EwS tumor cell states and regulatory vulnerabilities identified in human tumors pre- and post-therapy in preclinical models, further supporting translation of these findings toward therapeutic strategies. Citation Format: Abbe Pannucci, Elina Mukherjee, Jessica D. Daley, Shireen Sita Ganapathi, Elissa Boguslawski, Lea Surrey, Lauren Gutstein, Patrick Azar, Emily Stockfisch, Azfar Neyaz, Ivy John, Jennifer Picarsic, Yutaro Tanaka, Byron Butaney, Riaz Gillani, Brian D. Crompton, Katherine A. Janeway, Jaclyln Taroni, Jessica Davis, Damon Reed, Adam Shlien, Theodore W. Laetsch, Rajen Mody, Clémence Henon, Thomas G. Grünewald, Elizabeth R. Lawlor, Filemon Dela Cruz, Patrick J. Grohar, Jovana Pavisic, Ally Hawkins, Anthony R. Cillo, Kelly M. Bailey. The Sean Karl Cohort: An international single-cell RNAseq study of paired patient Ewing sarcoma specimens [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 643.