Citations

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 <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 < 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 Background: Liquid biopsy approaches for cancer detection often rely on tissue-specific methylation or fragmentation features to infer tumor origin. However, a pan-aerodigestive cancer detection strategy is clinically valuable given shared risk exposures, field cancerization, and frequent diagnostic ambiguity among lung, esophageal, and head & neck cancers. We hypothesized that advanced-stage disease exhibits convergent chromatin remodeling, producing a dominant malignancy-associated fragmentomic signal that supersedes subtler tissue-of-origin patterns. Methods: Whole-genome EM-seq (∼15×) was performed on plasma cfDNA from 120 patients with stage III/IV aerodigestive cancers (lung, esophageal, head & neck; squamous and adenocarcinoma) and 60 age-matched controls. Four fragmentomic modalities were assessed: (1) genome-wide fragmentation in 5-Mb bins (DELFI-like), (2) NMF spectral components, (3) 4-mer end motifs, and (4) promoter-centric nucleosome scores (Griffin). All preprocessing occurred strictly within each training fold of a repeated stratified 10-fold CV (100 repeats) to prevent data leakage. No test-sample information was used in training. Hyperparameters were tuned only within training partitions. Random Forest classifiers were trained under this fully nested scheme. Results: The multimodal classifier robustly detected advanced aerodigestive malignancies with a mean AUROC 0.86 and AUPRC 0.94. However, modality dissection revealed a clear performance hierarchy: nucleosome positioning (Griffin) alone achieved AUROC 0.85 and AUPRC 0.93, nearly matching the full integrated model, whereas end motifs performed poorly (AUROC 0.61). Biological interpretation demonstrated prominent nucleosome depletion centered at promoters of proliferation-associated genes, indicating a convergent epigenetic state of promoter opening across late-stage aerodigestive malignancies. Conclusions: Advanced aerodigestive cancers exhibit a dominant, convergent chromatin remodeling signature detectable in plasma cfDNA, driven primarily by altered nucleosome positioning. In late-stage disease, this shared malignancy-associated fragmentomic signal outweighs tissue-of-origin-dependent patterns. These findings highlight the utility of nucleosome-based fragmentomics not merely for detection, but for resolving diagnostic ambiguity in patients with indeterminate masses and for monitoring total tumor burden in high-risk aerodigestive malignancies. Citation Format: Axel Misael Hidalgo, Ayesha Hashmi, Jeff Szymanski, Pradeep Chauhan, Lilli Greiner, Faridi Qaium, Daniel J. Ma, David M. Routman, Katie M. Van Abel, Aadel A. Chaudhuri.. Convergent chromatin remodeling enables pan-aerodigestive detection of advanced malignancies in plasma cfDNA [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 3862.

ABSTRACT BACKGROUND Increasing evidence suggests that accurate prediction of Alzheimer’s disease (AD) symptom onset requires more than amyloid- and tau-centric biomarkers such as cerebrospinal fluid (CSF) Aβ42/40, total tau and p-tau181 and plasma p-tau217. Autosomal dominant AD (ADAD), caused by pathogenic PSEN1, PSEN2 and APP mutations with predictable age at symptom onset, presents a unique opportunity to characterize the chronological changes in proteins beyond amyloid and tau and clarify them as early biomarkers of disease onset or as biomarkers related to disease staging and progression monitoring. METHODS We measured 972 CSF samples corresponding to 484 participants of the Dominantly Inherited Alzheimer Disease Network (DIAN) using the NULISASeq 120 CNS Disease Panel. We first benchmarked the technology against gold-standard measurements followed by the identification of proteins that were differentially abundant in relation to mutation status and symptomatology. Next, we determined the chronological emergence of protein changes in relation to the estimated years to onset (EYO). Finally, we assessed whether specific protein measures improved the prediction of EYO in the ADAD. FINDINGS NULISA measurements were comparable to those previously published. We demonstrated that known early alterations in CSF amyloid and tau were followed by inflammatory and neurodegenerative responses suggesting that clinical manifestation of AD happens before the inflammatory processes is fully developed. Finally, we found a multi-protein composite approach for predicting EYO that outperformed single biomarker values. INTERPRETATION Our results suggest that the main CSF proteomic landscape changes in ADAD are due to the presence of a pathogenic mutation and occur prior to symptom onset. Improved performance of multi-protein composite to predict EYO compared to single biomarker values highlights the added value of multiplex proteomic signatures for biomarker panel development. FUNDING National Institute on Aging, Alzheimer’s Association, German Center for Neurodegenerative Diseases, Raul Carrea Institute for Neurological Research, Japan Agency for Medical Research and Development, Ministry of Health & Welfare and Ministry of Science and ICT, Republic of Korea, Spanish Institute of Health Carlos III.

Background: Eight Global Ophthalmology (GO) fellowship programs are available in the United States, and more than 30 U.S. GO fellows are now alumni. There are no standardized learning objectives for these programs, and fellows’ experiences vary widely between institutions. Purpose: To survey GO fellowship program directors in the United States to elucidate differences in learning objectives, duration of time abroad, funding sources, and other differences between GO fellowships. Methods: All program directors at all institutions with current GO fellowship programs in the United States were sent a 25-question questionnaire via email from October through December 2022. The questionnaire included distinct domains regarding the GO fellowship experience, care delivery, didactics, and best practices. Most questionnaire items were quantitative; 3 were qualitative. Responses to the quantitative and qualitative questions items were summarized descriptively. Results: All 10 program directors from the 8 GO fellowship programs that were current at the time of the survey participated. GO fellowship positions at most (88%) institutions were funded, in part, by the billing of care services provided by the fellows, with 50% of programs receiving supplemental funding from donations and 25% from nongovernmental organizations. Non-GO duties at the program home institutions constituted 29.5% of the time spent during the fellowships, on average. Policy advocacy occupies 2.3% of fellowship time, on average. Specific didactic topics covered in the GO programs and director perspectives on the pragmatic best practices for GO outreach varied considerably; however, inclusion of at least some public health topics and ethics appeared to be consistent among all of the programs. Conclusions: These findings provide insights into the landscape of GO fellowship programs in the United States, highlighting variations in funding, formal educational opportunities, and the allocation of time fellows spent working at the program home institution. Establishing standardized core competencies for fellows is recommended.

Abstract Cerebrospinal fluid (CSF) proteomics offers insights into molecular changes in aging and Alzheimer’s disease (AD). Key AD biomarkers, in particular amyloid-β (Aβ) and tau, in CSF are strongly associated with APOE genotype, the strongest genetic risk determinant of AD. To investigate how APOE genotype influences CSF proteome across AD pathology and age, we analyzed 362 neurology-related proteins and established AD biomarkers in CSF from 145 cognitively unimpaired participants in the Mayo Clinic Study of Aging. Importantly, our cohort is uniquely balanced across APOE genotypes, with similar representation of APOE2 carriers, APOE3/3 genotype, and APOE4 carriers. We identified several proteins, including lipid metabolism-related Lp-PLA2 and immune-related ITGAM, with strong APOE genotype-specific association. Notably, meta-analysis confirmed that ITGAM levels were consistently higher in APOE4 compared to APOE2 carriers across multiple cohorts and proteomic platforms. In addition, with increasing amyloid deposition, APOE4 carriers exhibited stronger immune responses, reflected by elevated ITGAM, TNF-α receptors, and IL-6, whereas APOE2 carriers showed attenuated responses. We further observed sex-specific effects among APOE2 carriers, characterized by distinct patterns in amyloid and CXCL11 levels. These findings suggest distinct mechanisms underlying APOE2’s protective and APOE4’s detrimental effects in brain aging and AD, paving for personalized diagnostics and interventions.