Citations

Context.— Optical genome mapping (OGM) represents a promising cytogenomic technology that detects structural variants, including fusions, rearrangements, copy number variants, and loss of heterozygosity, in a single assay. Unlike karyotyping, fluorescence in situ hybridization, or chromosomal microarray, OGM leverages long-molecule imaging to map the whole genome with high resolution. This positions OGM as a novel tool for constitutional and somatic/cancer genomics. However, its current and planned utilization in clinical and research settings remains unknown, necessitating further investigation. Objective.— To investigate the current utilization of OGM in clinical and research laboratories, assess its applications, and evaluate future utilization strategies. Design.— In 2024, a supplemental questionnaire was incorporated into 6 College of American Pathologists proficiency testing programs to evaluate OGM’s utilization. Results.— Of 921 returned questionnaires, 712 were analyzed after duplicates were removed. Sixty-seven (9.4%) currently offered OGM testing: 5.2% (37) for research only, 1.8% (13) for only clinical use, and 2.4% (17) for both. Future adoption plans showed 7.6% (53 of 700 laboratories) and 7.9% (55 of 700 laboratories) aiming to implement OGM clinically within 12 and 24 months, respectively. The most common applications included hematologic malignancies and constitutional/germline postnatal disorders, followed by prenatal testing. International laboratories demonstrated statistically higher utilization rates than domestic laboratories ( P = .001). Conclusions.— This first survey on OGM clinical utilization reveals its status as a niche technology, with 67 laboratories currently using it. Its primary clinical applications are in constitutional/germline analysis and hematologic malignancies. Although international laboratories led in 2024, 108 laboratories (domestic and international) plan clinical adoption within 24 months, signaling OGM’s potential for broader integration.

Background: The potential long-term effects of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) infection on the brain structure have not yet been fully elucidated. Even though existing studies have reported structural changes in the post-COVID-19 period, the results remain highly inconsistent and controversial. As such, identifying an imaging biomarker for post-COVID brains is still under investigation. This review aims to comprehensively summarize the structural MRI (sMRI) studies that focus on volumetric brain changes at least two weeks following COVID-19 infection. Methods: A systematic literature search was conducted on PubMed, SCOPUS, Web of Science, EMBASE, and Google Scholar up to 9 September 2025. Studies that utilized sMRI to assess volumetric brain changes post-COVID at greater than two weeks following infection were included. Exclusion criteria encompassed research involving pediatric or adolescent populations and imaging modalities other than sMRI. Preprints, reviews, case reports, case series and post-mortem studies were also excluded. Results: Forty-one studies satisfied the inclusion criteria and consisted of 2895 patients and 1729 healthy controls. Despite the wide variability in image acquisition protocols, data processing methods, and comorbidities between studies, multiple studies reported statistically significant volumetric reductions in the hippocampus, amygdala, thalamus, basal ganglia, nucleus accumbens and the cerebellum months to years after infection, especially in older hospitalized patients with severe COVID-19. Conclusions: The emerging literature reports long-term volume changes across various brain regions in individuals previously infected with COVID-19; however, the evidence is inconsistent. Specific imaging biomarkers following exposure to SARS-CoV-2 infection and the underlying mechanisms of these changes are yet to be identified. Future studies with harmonized imaging protocols, longitudinal designs, and integrated biomarker and clinical data are needed to define robust biomarkers and elucidate the pathophysiology of these findings.

Abstract Purpose This study investigates a novel optimization framework that integrates the newly developed MCF MKM relative biological effectiveness (RBE) model into intensity modulated particle therapy (IMPT) planning for carbon ion therapy. Unlike conventional RBE models such as MKM or LEM, the MCF MKM provides detailed microdosimetric information, which improves predictive accuracy of cell survival but elevates both memory and time requirement in the optimization process. Furthermore, to the implicit nature of the MCF MKM, the gradient information, which is essential in inverse planning, is hardly accessible. In response, a randomized gradient‐free optimization method (RGFM) was developed to mitigate the computational challenge and achieve improved RBE dose distributions. Materials and Methods An RBE dose optimization problem was formulated based on the discretized MCF MKM, known as the Abridged Microdosimetry Distribution Model (AMDM). The RGFM was derived to find feasible and high‐quality settings of monitor unit for IMPT plans without the need for explicit gradient calculations. To verify the clinical plausibility of the proposed method, it was tested on two clinical scenarios—prostate and brain cases in comparison with benchmark plans derived solely from physical dose optimization. Computational times and dose‐volume histograms (DVHs) for both physical and RBE doses were evaluated. Results The RGFM algorithm successfully optimized the MCF MKM‐based IMPT plans. Compared to the benchmark, the RBE dose distributions showed improved coverage of the target and reduced hot spots. Such improvements were observed to coincide with trade‐offs in physical dose distributions. The complexity of the MCF MKM extended the computational time, yet high‐quality solutions were attainable in a clinically reasonable timeframe. Multi‐field optimization (MFO) further enhanced target coverage and critical organ sparing over single‐field optimization (SFO). Conclusions This proof‐of‐principle study confirmed the feasibility of using a randomized gradient‐free method to optimize RBE dose based on the MCF MKM in IMPT planning for carbon ion therapy. The approach provides a pathway for clinical adoption of advanced RBE models, potentially leading to more biologically informed and effective carbon ion therapy treatments. Future work involves refining algorithms, incorporating parallel computing, and performing additional case studies to improve computational efficiency and generalizability.

Abstract Description A subset of follicular lymphoma patients has an early relapse with a poor outcome. We showed that this unfavorable group displays increased expression of IRF4, dysregulated immune signaling and an immunosuppressive microenvironment. However, little is known on the molecular mechanisms whereby IRF4 controls the crosstalk between B and T cells. To this aim, we leveraged Cγ1cre;irf4fl/fl mice that yield conditional deletion of irf4 (cKO) in germinal center B cells (GCB). After 10 days of immunization, cKO GCB showed significant increase of HLA-DR and CD40 expression, a skewed LZ:DZ ratio towards increased DZ, and suppression of plasma cells compared to WT. Upon irf4 deletion, we also found a significant increase of total CD4 and TFH cells and a decrease in Treg cells. To test if this effect was antigen-dependent, we cocultured sorted GCB from NP-OVA-immunized cKO and WT mice with CSFE-labeled OVA-specific OT-II CD4 T cells at a ratio of 2:1 for 5 days. We observed increased antigen specific proliferation of CD4 T cells with cKO GCB compared to WT. We then performed seahorse assay and mass spectrometry of the same GCB to define if IRF4-dependent B cell metabolic reprogramming influences immune responses. GCB cKO had lower glycolytic ECAR and increased intracellular glucose and non-essential amino acids than WT cells, suggesting a metabolic shift from glycolysis to the TCA cycle. Thus, IRF4 controls immune and metabolic signaling with functional effects on the B-T cell crosstalk. Funding Sources NCI K08CA279652, LRF Clinical Investigator Award (CDA 1020588), the Gerstner Family Career Development Award, the ASH Junior Faculty Scholar Award. Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)

Abstract Description tolerance is the “holy grail” in the fields of transplantation medicine and the treatment of autoimmune diseases. We previously reported that TIGIT+ B cells can efficiently control inflammatory responses while promoting regulatory T cell response via the ligation of CD155 expressed on both T cells and dendritic cells (DCs). Recent studies have also demonstrated that lack of TIGIT expression in B cells can lead to inflammation in the central nervous system in both humans and mice. These findings prompted us to explore whether TIGIT+ B cell therapy model could be developed for the treatment of inflammatory diseases. In this study, we report that TIGIT+ B cells can be generated with replication-incompetent recombinant Adv5 vectors designed to target CD21 on B cells. Those TIGIT+ B cells generated with our novel Adv5 vectors can efficiently control inflammatory T cell responses in vitro by directly acting on T cells and by regulating inflammatory function of DCs. The preclinical efficacy of TIGIT+ B cell therapy model and its underlying mechanisms of action are also investigated using an experimental autoimmune encephalomyelitis model. Data from this study support the clinical development of this novel TIGIT+ B cell therapy model for the treatment of inflammatory diseases. Funding Sources Mayo Clinic Cancer Center Topic Categories Therapeutic Approaches to Autoimmunity (THER)

Abstract Description Signal regulatory protein-α (SIRPα) is a key member of the “do-not-eat-me” signaling pathway and is expressed on intratumoral monocytes/macrophages in lymphoma. In this study, we found that SIRPα is also expressed by a subset of malignant B cells in lymphoma. SIRPα+ B cells have a memory phenotype with germinal center (GC) dark-zone features, and RNA velocity analysis showed that SIRPα+ B cells exhibit higher spliced transcripts confirming a more mature phenotype. SIRPα expression is substantially upregulated by treating lymphoma B cells with LPS or CpG and SIRPα+ B cells showed increased proliferation when compared to SIRPα- B cells, which was associated with reduced cellular autophagy. SIRPα+ B cells exhibited increased expression of BAFF signaling pathway molecules as the likely mechanism of increased proliferation and survival. Furthermore, in co-culture, SIRPα+ lymphoma B cells suppressed T-cell function and blocking SIRPa/CD47 signaling reversed T cell inhibition. Clinically, we found that a greater number of SIRPα+ B cells present in the diagnostic tumor biopsies of FL patients was associated with a significantly poorer overall survival. We conclude that SIRPα+ lymphoma B cells are a proliferative component of indolent lymphomas, are associated with T-cell suppression, and increased prevalence of these cells is associated with a poor prognosis. Targeting SIRPα+ B cells in lymphoma may therefore be a promising therapeutic strategy. Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)

Abstract Description The efficacy of immunotherapy for splenic marginal zone lymphoma (SMZL) remains limited due to the strong immune suppression present in the tumor microenvironment (TME). Tregs play a key role in maintaining TME homeostasis by suppressing effector T cells and malignant B cells. Previously, we identified two Treg subsets CD26+ and CD161+ in SMZL. CD161+ Tregs were more effective at suppressing both CD8+T cells and malignant B cells, whereas CD26+Tregs primarily inhibited CD8+T cells. Patients with higher levels of CD26+ Tregs and fewer CD161+ Tregs tend to have worse outcomes. In this study, we found that cytokine-inducible SH2-containing protein (CISH), a known negative regulator of immune activation, is highly expressed in CD26+Tregs compared to CD161+ Tregs. Co-culturing B cells enhanced the expression of CISH and CD26 in CD4+CD25- Treg cells, knockdown of CISH in Tregs reduced CD26 expression and their immune suppression activity of CD8+T cells, while CRISPR knockout of CISH in Karpas 299 cells led to higher expression CD70, a molecule associated with less immunesuppression. Our findings suggest that increased CISH expression in Tregs could result in increased immune suppression and unfavorable outcome in SMZL, suggesting CISH is a potential therapeutic tagrget in SMZL by dempening immunosuppressive property of the Treg cells hence boosting the antitumor immunity. Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)

Artificial intelligence (AI) is increasingly shaping pediatric spine care, leveraging its rapid advancements in healthcare to improve efficiency, accuracy, and disease understanding. Moreover, machine learning and deep learning excel at detecting complex patterns. This holds promise in processing spinal deformity data, with the potential to surpass traditional statistical methods in predictive accuracy. Challenges persist, however, including unclear clinical implementation guidelines, limited model transparency, and ethical concerns surrounding data privacy and bias. Small sample sizes and the need for larger, diverse datasets further complicate integration. In order to realize AI’s transformative potential in pediatric spine care, these critical obstacles must be addressed for effective and ethical clinical adoption. This review examines the role of AI through applications such as image sorting, surgical outcome prediction, forecasting of spinal curve progression, and vertebral volumetric analysis using deep reasoning. It also explores possible intraoperative contributions from AI, including robotics and optimized screw trajectory planning, and the potential of large language models in clinical practice.

Abstract Background The RefleXion X1 is a novel PET/CT‐guided ring gantry linac that introduces unique geometry and workflow compared to conventional systems. Existing QA guidelines (AAPM TG‐142, 148, 306) cover standard linacs and tomotherapy but do not address this platform's needs. Therefore, an automated daily QA solution is required to ensure accurate output, imaging guidance, and couch positioning, which motivated the development and evaluation of the workflow presented in this study. Purpose To develop and evaluate an automated, efficient, and comprehensive daily quality assurance (QA) workflow for a novel PET/CT‐guided ring gantry linear accelerator (RefleXion X1), incorporating tests for dosimetry, imaging guidance, and couch positioning accuracy. Methods An IMRT QA plan was designed following the CT scan of the TomoDose 2D diode detector array (Sun Nuclear, Melbourne, FL) within the RefleXion treatment planning system (TPS). Several spherical targets of varying sizes were contoured to conform the dose distribution to these targets and evaluate beam output, laser localization, profile constancy, and CT‐MV isocenter coincidence. Linear models correlating spatial location of dose peak with intentional shifts in different directions were developed and integrated into an in‐house analysis software, iQA, written in C#. The software was validated for robustness and successfully implemented in clinical practice. Results Validation with 42 intentional shifts showed submillimeter accuracy, with mean deviations of 0.2 mm (X), 0.1 mm (Y), and 0.79 mm (Z), and R 2 values ≥ 0.98. Over 1 year, daily QA data showed stable output constancy (1.006 ± 0.016), left/right target dose constancy (1.007 ± 0.005 and 0.996 ± 0.004), and consistent CT‐MV isocenter offsets (–0.335 ± 0.23 mm in X, 0.19 ± 0.19 mm in Y, and –0.544 ± 0.36 mm in Z). The software also detected a gradual output drift in between, prompting a timely linac adjustment. Conclusion This fully automated, single‐delivery QA workflow enables efficient and robust evaluation of multiple IGRT performance parameters. It improves standardization, reduces human error, and reliably monitors long‐term machine stability. The tools and methodology may be adopted by other clinics seeking a practical and automated daily QA solution. Future developments will focus on incorporating PET QA and rotational couch validations to further enhance the system's comprehensiveness and adaptability.