Citations

Abstract Recent advances in long-read transcriptome sequencing enable high-throughput profiling of full-length RNA isoforms in bulk, single-cell, and single-nucleus samples. However, long-read datasets typically contain a mixture of complete and partial transcripts, leading to pervasive ambiguity in read-to-isoform assignment and complicating accurate isoform identification and quantification, particularly in the absence of reliable reference annotations. These challenges are further amplified in single-cell and single-nucleus samples, where coverage is sparse and transcriptional heterogeneity is high. Here, we present the Long Read Alignment Assembler (LRAA), a unified and versatile computational framework for isoform identification and quantification from long-read RNA sequencing data across bulk, single-cell, and single-nucleus transcriptomic samples. LRAA combines splice-graph based structural modeling with expectation maximization based optimization to probabilistically resolve ambiguous read assignments and improve isoform abundance estimation. The framework supports quantification-only, reference-guided, and fully reference-free (de novo) modes of analysis within a single methodological paradigm. We benchmarked LRAA using both simulated and genuine long-read datasets spanning sequencing standards and whole transcriptomes. Central to this evaluation is a novel benchmarking strategy based on Multiplexed Overexpression of Regulatory Factors (MORFs), which provides biologically expressed, barcoded isoforms with unambiguous read-level ground truth. Across all benchmarks, including MORFs, synthetic spike-ins, and whole-transcriptome datasets, LRAA consistently outperformed state-of-the-art methods in isoform identification accuracy, sensitivity, and expression quantification. Finally, we demonstrate the biological utility of LRAA by resolving cell-type-specific isoform usage across peripheral blood immune cell populations and by detecting a pathogenic cryptic isoform of STMN2 with associated transcriptional changes in single-nucleus RNA-seq data from frontal cortex tissue of an individual with frontotemporal dementia (FTD). Together, these results establish LRAA as a robust and general solution for resolving transcript diversity in complex biological systems, from development to disease.

Neutrophils and neutrophil extracellular traps (NETs) contribute to early neuromyelitis optica (NMO) histopathology initiated by IgG targeting astrocytic aquaporin-4 (AQP4) water channels. Yet, the mechanisms underlying neutrophil recruitment and their pathogenic roles in disease progression remain unclear. To investigate molecular-cellular events preceding classical complement cascade activation in a mouse NMO model, we continuously infused, via spinal subarachnoid route, a non-complement-activating mouse monoclonal AQP4-IgG. Parenchymal infiltration of netting neutrophils containing C5a ensued with microglial activation and motor impairment but no blood-brain barrier leakage. Motor impairment and neuronal dysfunction both reversed when AQP4-IgG infusion stopped. Two-photon microscopy and electron microscopy–based reconstructions revealed physical interaction of infiltrating neutrophils with microglia. Ablation of either peripheral neutrophils or microglia attenuated the motor deficit, highlighting their synergistic pathogenic roles. Of note, mice lacking complement receptor C5aR1 exhibited reduction in neutrophil infiltration, microglial lysosomal activation, neuronal lipid droplet burden, and motor impairment. Pharmacological inhibition of C5aR1 recapitulated this protection. Immunohistochemical analysis of an NMO patient’s spinal cord revealed disease-associated microglia surrounding motor neurons in nondestructive lesions. Our study identifies neutrophil-derived C5a signaling through microglial C5aR1 as a key early driver of reversible motor neuron dysfunction in the precytolytic phase of NMO.

Abstract Measurement of D-dimer, a fibrin degradation product, is crucial for diagnosing thrombotic and fibrinolytic conditions. Despite its expanding utility, D-dimer testing faces challenges due to varying assay methodologies and nonstandardized reporting. To understand D-dimer reporting practices, the College of American Pathologists Hemostasis and Thrombosis Committee analyzed proficiency testing data from D-dimer surveys conducted between 2020 and 2023 across multiple laboratories. The data demonstrate that laboratories commonly report units that differ from the assay package insert when reporting their proficiency testing results. We sought to assess variability in reporting practices and opportunities for improvement in D-dimer reporting amongst participants. To accomplish this, we harmonized all D-dimer results to ng/mL fibrinogen equivalent units from one distributed sample and assessed distinct populations of entries per instrument/reagent combination. Notable trends emerged from this analysis. Data from laboratories using the same instrument/reagent combinations clustered around different means, suggesting issues with unit reporting and/or conversion. Entries reported in mg/L or ug/mL D-dimer units commonly exhibited significant deviations from the dominant population. For one instrument/reagent combination, most reported values differed by approximately twice the certificate of analysis value. This analysis highlights potential issues with D-dimer reporting in proficiency testing. Whether these issues translate into issues with clinical D-dimer reporting requires further study.

Abstract Background Long-acting injectable buprenorphine (LAIB) has been positioned as a potentially transformative option for opioid use disorder (OUD), in part because patient experiences reported in qualitative studies emphasize reduced daily burden, increased “freedom,” reduced stigma, and fewer pressures related to diversion—while also noting barriers such as insufficient information, early adverse experiences, and concerns about coercion. Methods We conducted a cross-sectional online survey of adults recruited from the Behavioral Health Research Panel (BHRP). Eligibility included age ≥18, English literacy, and OUD diagnosis or problematic opioid use within the past 5 years. Survey content assessed buprenorphine experience, knowledge and attitudes toward LAIB, attribute preferences, and open-text feedback. Descriptive statistics were generated; analyses were stratified by buprenorphine experience (experienced vs naïve). Results Among 105 participants, 82.9% reported prior buprenorphine use, and 17.1% were buprenorphine-naïve. Overall, 53.3% preferred a long-acting injection regimen (weekly/monthly/3-monthly) versus 46.7% preferring a daily oral tablet/film. Convenience and adherence-related themes (e.g., not missing doses, fewer visits) drove LAIB preference, while oral-route preference and concerns about side effects and safety were prominent among those favoring oral formulations. Conclusions In this national convenience sample, preferences were nearly evenly split between daily oral and long-acting injectable buprenorphine regimens, with a slight overall preference for LAIB. Findings align with the qualitative literature, emphasizing the practical and psychosocial benefits of LAIB, alongside persistent needs for improved education, shared decision-making, and attention to tolerability, safety perceptions, and cost/coverage barriers.

Abstract Background Recurrent pericarditis (RP) predominantly shows features consistent with IL-1-mediated chronic autoinflammatory disease (1-4). A recent analysis suggested that supplementing anakinra with colchicine incrementally reduced pericarditis recurrence vs. anakinra alone (5). Rilonacept (a weekly IL-1α and IL-1β cytokine trap with 6-week washout) prevents engagement with IL-1 receptor, inhibiting both IL-1α and IL-1β activity (6). The Phase 3 trial RHAPSODY demonstrated rilonacept efficacy in two independent analyses: Randomized Withdrawal (RW) and Long-Term Extension (LTE) periods (7,8). Purpose Assess long-term recurrence-free persistence with rilonacept as monotherapy in pts with RP during the combined RW and LTE periods of RHAPSODY. Methods Post-hoc analysis. Freedom from recurrence on rilonacept monotherapy was quantified using the Kaplan-Meier (KM) method from RW start (if randomized to rilonacept) or from initiation of bailout rilonacept (if randomized to placebo) until the end of treatment. Prespecified recurrence adjudication criteria were pericarditis pain (numerical rating scale [NRS]) ≥4 plus C-reactive protein (CRP) ≥1 mg/dL. Per RHAPSODY protocol, background therapies were discontinued during the Run-In Period before randomization. In pts treated with rilonacept, concomitant colchicine was not added during the RW period. In the LTE, 6.8% (5/74) of pts added colchicine: one for 2 days of chest pain without CRP elevation, 4 in the absence of chest pain, CRP elevation, or recurrence; these 5 pts were censored in the KM curve at 6 days after last rilonacept dose or at colchicine initiation (whichever was first). One additional pt added colchicine prophylactically before an intentional rilonacept treatment interruption for elective cardiac surgery and experienced a recurrence after this interruption; this pt was not censored from the recurrence-free persistence analysis at colchicine initiation in order to capture this event. Results 74 pts (mean [SD] age 43.9 [15.7] years, 83.8% idiopathic pericarditis, mean [SD] disease duration 2.5 [3.2] years) were analyzed over three years. Rilonacept was well tolerated. Recurrence-free persistence was 95.9% (n=71/74) while receiving rilonacept as monotherapy (Figure 1). The three observed adjudicated recurrences were each associated with temporary interruptions of 1-3 doses of rilonacept. Conclusions Rilonacept as monotherapy provided recurrence-free persistence over the three-year trial duration when used continuously without interruption; pericarditis recurrences occurred only after interruptions. These findings support evidence-based use of rilonacept as monotherapy, minimizing the need for adjunctive treatments and reducing polypharmacy in long-term RP management. Further investigations are warranted to address how to assess pts as candidates for long-term treatment with rilonacept and when to cease rilonacept treatment.

Abstract Glioblastoma (GBM) remains the most aggressive primary adult brain cancer with limited therapeutic options. Our prior research demonstrated that androgen receptor antagonists (ARAs) enhance survival in GBM mouse models by preferentially suppressing glioma stem cells. This study investigates the potential of ARAs as radiosensitizers in combination with radiotherapy (RT). Combined effects of ARAs and RT were evaluated using an orthotopic GBM mouse model. RNA-Seq and TCGA analyses delineated AR-associated regulatory networks, while integrated cellular and molecular approaches utilizing human and mouse GBM cell lines, as well as in patient-derived primary high-grade glioma cultures, interrogated signaling and immune paradigms. ARA treatment induced G2/M cell cycle arrest, apoptosis, and downregulated DNA repair genes, with AR expression correlating with the DNA repair and TGF-β pathway. In both immortalized GBM cell lines and primary high-grade glioma cultured cells, ARAs in combination with RT showed only a modest enhancement of radiosensitivity. However, in an orthotopic GBM mouse model, ARA + RT demonstrated a strong synergy, achieving 100% long-term survival, compared to less than 50% with ARA alone and 0% with RT alone. Mechanistically, ARA modulated the TGF-β pathway, durably switching from Smad3 linker to c-terminal phosphorylation (pSmad3C) and inhibiting LIF/STAT3 axis. Distinct TGF-βs ligand expression patterns were observed in ARA-treated GBM cells. A protein–protein interaction noted between AR and Smad3, which was disrupted following ARA treatment, leading to elevated protein levels and nuclear localization of pSmad3C (S423/425), indicating normalization/activation of the TGF-β/pSmad3C-dependent anti-tumorigenic cascade. Comprehensive analyses in GBM cell lines and mouse model tissues demonstrated pathway reprogramming characterized by elevated TGF-β2 and increased pSmad3C. Tissue analysis revealed immune activation in the tumor microenvironment, while peripheral blood and spleen showed systemic immune responses following ARA + RT. Our study provides novel insights into how ARAs enhance RT efficacy through immunomodulation involving TGF-β/pSmad3C cascade, offering therapeutic implications in GBM.

Abstract Background Renal denervation (RDN) has emerged as a promising therapeutic adjunct for the management of hypertension, yet its efficacy in the long term, particularly in patients with hypertension and concurrent renal insufficiency, remains to be fully elucidated. This study was designed to evaluate the sustained impact of RDN on blood pressure control, renal function, and cardiovascular outcomes in hypertensive patients with pre-existing renal impairment over an extended follow-up period. Methods We conducted a single-center, single-arm, real-world retrospective study involving patients with hypertension and chronic kidney disease (CKD) stages 3-4 who underwent RDN at a hospital between 2011 and 2016. Comprehensive baseline data, including demographic information, comorbidities, and medication history, were meticulously recorded. Long-term follow-up assessments were performed at 1, 5, and 11.5 years post-RDN to monitor changes in office and home blood pressure, 24-hour ambulatory blood pressure results, renal function, and the incidence of cardiovascular events and mortality. Results A total of 20 participants completed the long-term follow-up, with a mean age of 51.7 ± 14.5 years (35% female), and a median follow-up duration of 11.5 years. At baseline, the cohort presented with an average office systolic blood pressure of 183.8 ± 18.6 mmHg and a diastolic blood pressure of 104.7 ± 17.0 mmHg. Following RDN, participants experienced a significant reduction in blood pressure, with an average decrease of -37.94/-20.38 mmHg (P < 0.001) compared to baseline. Additionally, ambulatory systolic and diastolic blood pressures were reduced by 16.87 ± 9 mmHg (P < 0.001) and 9.88 ± 4.05 mmHg (P < 0.001) 11.5 years after the procedure, respectively. The study also revealed a substantial reduction in the need for antihypertensive medications (P < 0.001) and a decrease in average heart rate (P = 0.046) following renal denervation. Assessments of renal function, as measured by estimated glomerular filtration rate and creatinine levels, were consistent with expected age-related decline. Importantly, no significant adverse events associated with RDN were observed in the long-term follow-up. Over the 11.5-year period, the cardiovascular mortality rate and overall mortality were 10% and 20%, respectively. Conclusion This long-term follow-up study demonstrates that RDN is a safe and effective intervention for managing hypertension in patients with renal impairment.

Abstract Background Cancer therapies have prolonged survival in lymphoma. However, lymphoma patients may develop significant coronary artery disease (CAD), which may be treated by percutaneous coronary intervention (PCI). The characteristics and outcomes of lymphoma patients treated by PCI are not well studied. Methods We reviewed lymphoma patients undergoing PCI at our institution between 2010 and 2020 and compared them to a cohort without cancer. Patient characteristics and predictors of long-term mortality and major adverse cardiac events (MACE) (death, myocardial infarction, target lesion revascularization) were studied using descriptive statistics and survival analysis utilizing a Cox proportional hazards model. Results Of the 11,953 patients in the study cohort, 83 had a history of lymphoma meeting study criteria. Lymphoma patients, as compared to non-lymphoma patients were similar with respect to age, sex, hypertension, diabetes, hyperlipidemia, prior MI, and prior PCI (all p=ns). Over a median follow-up of 3.9 (1.0, 5.0) years, the mortality at 5 years was higher in lymphoma versus non-lymphoma patients (47.5% vs 29.8%) (P=0.005) (Figure). After adjusting for age, sex, hypertension, diabetes, shock, smoking status, heart failure, and chronic renal disease, lymphoma was an independent predictor of mortality (OR 1.59; 95% CI 1.07-2.36, p=0.02). Lymphoma was not independently associated with MACE. Discussion Lymphoma patients undergoing PCI have significantly lower survival rates than non-cancer controls. After accounting for important cardiac risk factors, lymphoma was independently associated with higher long term mortality.

PURPOSE Despite evidence of diagnostic accuracy but unclear long-term clinical benefit, national utilization patterns of prostate-specific membrane antigen positron emission tomography (PSMA-PET) are undefined. METHODS We conducted a serial cross-sectional study to evaluate the use of PET imaging among commercial insurance beneficiaries with prostate cancer using administrative claims from deidentified Blue Cross Blue Shield Axis database. Eligible patients included prevalent and incident prostate cancer cases. We calculated the proportions undergoing PET imaging in semiannual periods from January 1, 2016, through December 31, 2024. We examined the association between regional-level contextual sociodemographic and health care characteristics, and regional use of PSMA-PET imaging in 2024. RESULTS A total of 514,750 male beneficiaries age 40-89 years with prostate cancer were identified between 2016 and 2024. The proportion of individuals with prostate cancer undergoing PET imaging increased from 4.5 [95% CI, 4.1 to 4.9] per 1,000 in the first half of 2016 to 77.6 (95% CI, 76.2 to 79.1) per 1,000 in the second half of 2024, P < .001. Increases in PET were driven by uptake of PSMA-PET following approval in 2021, which increased from 0.8 (95% CI, 0.6 to 0.9) per 1,000 in the second half of 2021 to 77.0 (95% CI, 75.5 to 78.5) per 1,000 in the second half of 2024, P < .001. PSMA-PET use in 2024 was higher in regions with greater education (99.3 v 114.6 per 1,000 in lowest [Q1] v highest [Q4] educated) and income (95.4 v 112.3 per 1,000 in Q1 v Q4 income) measures, P < .001. CONCLUSION PSMA-PET was rapidly incorporated into clinical practice among commercial insurance beneficiaries with prostate cancer with higher adoption in geographic regions with higher income and education.

Abstract Background Long-acting injectable buprenorphine (LAI-BUP) is safe and effective, however is dramatically underutilized in comparison to oral formulations. Little is known regarding how buprenorphine prescribers view LAI-BUP, and which medication attributes they prioritize when selecting treatment for opioid use disorder (OUD). Methods A secondary analysis of a national, cross-sectional online survey of U.S. physicians who prescribe buprenorphine for OUD was conducted. Respondents reported OUD caseload, LAI-BUP use, and the importance of medication attributes relevant to treatment selection (e.g., efficacy, safety, ease of administration, ease of prescribing, and administrative requirements). Providers were categorized as no LAI-BUP use or, among LAI-BUP prescribers, Low vs High use based on a median split. Group comparisons used chi-square (or Fisher’s exact) tests for categorical variables and Jonckheere–Terpstra tests for ordinal responses. Results Among 125 respondents, 39 (31.2%) reported no patients receiving LAI-BUP. The remaining 86 (68.8%) were LAI-BUP prescribers, split evenly into Low and High (n’s=43; 34.4%) groups using a median cut of 23.2%. LAI-BUP use did not differ meaningfully by specialty, region, or practice setting. Greater LAI-BUP use was reported by providers with larger OUD panels. Ratings of key medication attributes were uniformly high. Conclusions LAI-BUP remains underused, with uptake highest among clinicians managing larger OUD caseloads. Measured attitudes toward medication attributes did not explain these differences. Future work should assess clinic workflow, staffing, reimbursement, and REMS burden, testing targeted implementation strategies using mixed-methods trials. Identifying what shifts clinicians from no use to low and high use may guide scalable implementation interventions.