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PathoCellBench: A comprehensive benchmark for cell phenotyping
No full textDigital pathology has seen the advent of a wealth of foundational models (FMs), yet to date their performance on cell phenotyping has not been benchmarked in a unified manner. We therefore propose PathoCellBench: A comprehensive benchmark for cell phenotyping on Hematoxylin and Eosin (H&E) stained histopathology images. We provide both PathoCell, a new H&E dataset featuring 14 cell types identified via multiplexed imaging, and ready-to-use fine-tuning and benchmarking code that allows the systematic evaluation of multiple prominent pathology FMs in terms of dense cell phenotype predictions in a range of generalization scenarios. We perform extensive benchmarking of existing FMs, providing insights into their generalization behavior under technical vs. medical domain shifts. Furthermore, while FMs achieve macro F1 scores > 0.70 on previously established benchmarks such as Lizard and PanNuke, on PathoCell, we observe scores as low as 0.20. This indicates a much more challenging task not captured by previous benchmarks, establishing PathoCell as a prime asset for future benchmarking of FMs and supervised models alike. Code and data are available on GitHub
Staufen2 modulates the temporal dynamics of human neurogenesis in vitro
Get PDFRNA-binding proteins (RBPs) play a central role in post-transcriptional regulation during brain development, yet their specific functions in coordinating human neural lineage decisions remain poorly understood. Here, we investigate for the first time the role of the double-stranded RBP Staufen2 (STAU2) in human neurogenesis. Characterization of STAU2 knockout iPSC derived cells using scRNA-seq shows that loss of STAU2 disrupts neuroepithelial cell identity and accelerates neural differentiation by altering the activity of key transcription factors and driving early metabolic transitions. Additionally, STAU2 regulates the expression of miRNA host genes and alters miRNA-mediated post-transcriptional control in progenitor cells, which exerts additional effects on STAU2 regulated gene regulatory networks. These changes result in neural progenitor exhaustion, unstructured neural rosettes, and reduced organoid size. Together, our work uncovers a previously unrecognized role for STAU2 as a central regulator of early human neurogenesis, acting through both miRNA-mediated and transcriptional pathways to coordinate progenitor maintenance and neuronal fate specification
Prime editing corrects the dilated cardiomyopathy causing RBM20-P633L-mutation in human cardiomyocytes
Get PDFPrime editing (PE) is an innovative next-generation gene editing tool that has therapeutic potential in post-mitotic organs, such as the human heart. However, its applicability and efficiency in non-proliferating cells, e.g., human cardiomyocytes, is not yet established. Here, we apply PE directly in cardiomyocytes differentiated from human induced pluripotent stem cells (hi-CMs) carrying dilated-cardiomyopathy-causing mutations. A target array (TA) containing the mutations LMNA(K117fs) (348–349insG), RBM20(P633L) (c.1898 C>T), and RBM20(R634Q) (c.1901 G>A) in the safe-harbor locus AAVS1 in HEK293T cells served as a screening platform for prime editing gRNAs (pegRNAs). The pegRNA screen yielded a set of efficient pegRNAs targeting the respective mutations. Using the PE4 system to correct the RBM20(P633L)-mutation, we achieved 34.8% T-to-C editing efficiency on average in homozygous P633L/P633L-hi-CMs while maintaining low off-target editing. PE restored RBM20’s nuclear localization and normalized cardiac splicing of the calcium-/calmodulin-dependent protein kinase II delta (CAMK2D) transcript. We combine a detailed pegRNA screening assay in an easy-to-transfect HEK293T system (TA-HEK) with subsequent functional validation of PE in hi-CMs carrying patient-derived mutations. This strategy yielded the first PE-mediated phenotypic rescue in a human post-mitotic model of DCM and paves the way for an in vivo strategy to treat RBM20(P633L)-mediated DCM and other inherited cardiac diseases
Large language models for patient education prior to interventional radiology procedures: a comparative study
Get PDFPURPOSE: This study evaluates four large language models' (LLMs) ability to answer common patient questions preceding transarterial periarticular embolization (TAPE), computed tomography (CT)-guided high-dose-rate (HDR) brachytherapy, and bleomycin electrosclerotherapy (BEST). The goal is to evaluate their potential to enhance clinical workflows and patient comprehension, while also assessing associated risks. MATERIALS AND METHODS: Thirty-five TAPE, 34 CT-HDR brachytherapy, and 36 BEST related questions were presented to ChatGPT-4o, DeepSeek-V3, OpenBioLLM-8b, and BioMistral-7b. The LLM-generated responses were independently assessed by two board-certified radiologists. Accuracy was rated on a 5-point Likert scale. Statistics compared LLM performance across question categories for patient-education suitability. RESULTS: DeepSeek-V3 attained the highest mean scores for BEST [4.49 (± 0.77)] and CT-HDR [4.24 (± 0.81)] and demonstrated comparable performance to ChatGPT-4o for TAPE-related questions (DeepSeek-V3 [4.20 (± 0.77)] vs. ChatGPT-4o [4.17 (± 0.64)]; p = 1.000). In contrast, OpenBioLLM-8b (BEST 3.51 (± 1.15), CT-HDR 3.32 (± 1.13), TAPE 3.34 (± 1.16)) and BioMistral-7b (BEST 2.92 (± 1.35), CT-HDR 3.03 (± 1.06), TAPE 3.33 (± 1.28)) performed significantly worse than DeepSeek-V3 and ChatGPT-4o across all procedures. Preparation/Planning was the only category without statistically significant differences across all three procedures. CONCLUSION: DeepSeek-V3 and ChatGPT-4o excelled on TAPE, BEST, and CT-HDR brachytherapy questions, indicating potential to enhance patient education in interventional radiology, where complex but minimally invasive procedures often are explained in brief consultations. However, OpenBioLLM-8b and BioMistral-7b exhibited more frequent inaccuracies, suggesting that LLMs cannot replace comprehensive clinical consultations yet. Patient feedback and clinical workflow implementation should validate these findings
CAR-T cells targeting CD19 for the treatment of ANCA vasculitis
Get PDFAutoimmune ANCA-associated vasculitis (AAV) and glomerulonephritis is characterized by the presence of autoantibodies (so-called ANCA = anti-neutrophil cytoplasmic autoantibodies), which, by binding to the body's own antigens, lead to damaged blood vessels (vasculitis) and subsequently to organ damage, particularly of the kidneys. The primary endogenous antigens are the enzymes proteinase 3 (PR3) and myeloperoxidase (MPO) expressed by neutrophil granulocytes and monocytes. In addition to the autoantibodies, both T-cellular response to those autoantigens and monocyte/macrophage-mediated processes play a decisive role. Since conventional therapy is based on the widespread suppression of the immune system, susceptibility to infections or the development of cancer are possible side effects. Furthermore, not all patients respond to conventional therapy or despite responding first suffer multiple relapses. Therefore, there is a need for alternative treatment strategies and one promising option is the use of CD19-targeting CAR-T cells
Rbm20 antisense oligonucleotides alleviate diastolic dysfunction in a mouse model of cardiometabolic heart failure (HFpEF)
Get PDFAIMS: Heart failure with preserved ejection fraction (HFpEF) is prevalent, deadly, and difficult to treat. Risk factors such as obesity and hypertension contribute to cardiac inflammation, metabolic defects, and pathological remodelling that impair ventricular filling in diastole. Titin based stiffness is a main determinant of diastolic function and can be adjusted by the splicing regulator RNA binding motif protein 20 (RBM20). Inhibition of RBM20 using antisense oligonucleotides (ASOs) induces expression of compliant titin isoforms, which reduce stiffness. However, dose finding and documenting utility in primarily cardiometabolic disease remains challenging. METHODS AND RESULTS: Here, we optimized RBM20-ASO dosing in a HFpEF mouse model that closely mimics human disease, characterized by metabolic syndrome and comorbidities, but without primary defects in titin or RBM20. Partial inhibition of RBM20 (∼50%) selectively increased compliant titin isoforms, improving diastolic function while preserving systolic performance. This intervention reduced left ventricular stiffness, enhanced relaxation, and mitigated cardiac hypertrophy, despite ongoing systemic comorbidities. CONCLUSION: Our findings demonstrate that targeting titin stiffness with Rbm20-ASOs can serve as an alternative or adjunctive therapeutic strategy for HFpEF to restore cardiac function and prevent further organ damage. The approach may offer benefits even in the presence of phenotypic heterogeneity and unresolved systemic comorbidities
Local and systemic responses to low-intensity cycling with blood flow restriction compared to high-intensity cycling: a randomized crossover study
Get PDFDespite growing interest in blood flow restriction (BFR) for enhancing training adaptations, its acute impacts on local and systemic physiological stress remain incompletely understood. This study compared the metabolic and perceptual responses of low-intensity cycling (LI) with BFR (LI + BFR) to both LI and high-intensity (HI) cycling without BFR, matched for time and external work. Ten males (26.9 ± 4.6 years) completed LI (20 min at 55% peak aerobic power output, PPO), LI + BFR (with 50% limb occlusion pressure), and HI (10 × 1 min at 90% PPO interspersed with 1-min recovery at 20% PPO) protocols in a randomized cross-over design. Interstitial metabolic responses were assessed via microdialysis in the vastus lateralis; systemic blood responses were evaluated via venous blood gas analysis. Cardiorespiratory responses, including heart rate, oxygen uptake, and ventilation, were continuously monitored during exercise. Serum creatine kinase (CK) and lactate dehydrogenase (LDH) were measured as indirect markers of muscle damage, and perceptual responses were documented. Muscle interstitial lactate and pyruvate were highest in HI, followed by LI + BFR, and lowest in LI (p < 0.05). Systemic blood and cardiorespiratory responses were comparable between LI + BFR and HI and exceeded LI (p < 0.05), while electrolyte shifts occurred across all conditions (p < 0.001) without between-condition differences. All protocols increased CK and LDH 24–48 h post-exercise, with the greatest increases in HI (p < 0.05). Perceived exertion and pain were higher in LI + BFR than in other conditions (p < 0.05). In conclusion, BFR intensifies local and systemic stress during LI and may be a potent strategy to promote muscle adaptive stimulus. However, when time and total external work are matched, high mechanical loading appears more effective in inducing local stress, which may be essential for further muscular adaptation processes
Mechanically-gated currents in mouse sensory neurons lacking PIEZO2
Get PDFTouch sensation starts with the opening of mechanically-gated activated ion channels at neuroglial endings of mechanoreceptors in the skin. The function of around half of low threshold mechanoreceptors is dependent on the presence of the mechanically gated ion channel PIEZO2. It has been reported that particularly rapidly-adapting mechanosensitive currents (RA-currents) in the cell bodies of acutely cultured sensory neurons are dependent on PIEZO2. Here we re-examined this question by making a quantitative study of mechanically-gated currents activated by substrate deflection in sensory neurons lacking PIEZO2. We characterized mechanically-gated currents from embryonic and post-natal sensory neurons, taken from global Piezo2(-/-) or Piezo2 conditional knockouts (Piezo2(cko)), respectively. Surprisingly in both models, Piezo2 gene deletion was not associated with any significant reduction in the sensitivity or incidence of mechanosensitive currents compared to wild type controls. There was, however, a moderate reduction in the incidence of RA-currents with very fast activation and inactivation kinetics in both embryonic Piezo2(-/-) and juvenile Piezo2(cKO) mice. These results show that PIEZO2 channels are not the only mechanosensitive channels mediating RA-currents in sensory neurons. Furthermore, our data suggest that the phenotypes associated with Piezo2 loss of function alleles may sometimes be due to secondary effects of gene deletion, for example, by changing the developmental trajectory of sensory neurons. Emphasis should be put on the diversity of mechanosensitive ion channel function in sensory neurons which needs to be further elucidated. SIGNIFICANCE: The mechanosensitive ion channel PIEZO2 has been proposed to be the major mechanically-gated ion channel for the transduction of touch. We used patch-clamp electrophysiology to measure mechanically gated currents in sensory neurons lacking PIEZO2 channels using two distinct genetic strategies. Piezo2 gene deletion was associated with a moderate reduction in the frequency of very rapidly inactivating mechanosensitive currents in early post-natal sensory neurons. No significant reduction in the sensitivity or incidence of mechanosensitive currents was observed. These data challenge the idea that PIEZO2 channels are the main transducers of force in sensory neurons, at least via substrate deflection. Other interpretations of loss of function phenotypes, including the possibility that early loss of PIEZO2 could alter developmental trajectories of sensory neurons to impair mechanoreceptor function, should be considered
Detecting early kidney allograft fibrosis with multi-b-value spectral diffusion MRI
Get PDFKidney allograft fibrosis is a manifestation of chronic kidney disease (CKD) and predicts functional decline, and eventual allograft failure. This study evaluates whether spectral diffusion magnetic resonance imaging (MRI) detects early development and mild/moderate fibrosis in kidney allografts. In a prospective two-center study of kidney allografts, pathologic interstitial fibrosis and tubular atrophy (IFTA) was scored and eGFR was calculated from serum creatinine. Multi-b-value diffusion-weighted imaging (DWI) (bvalues=[0, 10, 30, 50, 80, 120, 200, 400, 800mm(2)/s]) was post-processed with spectral diffusion, intravoxel incoherent motion (IVIM), and apparent diffusion coefficient (ADC). Relationships between imaging parameters and biological processes were measured by Mann-Whitney U-test and Spearman’s rank; diagnostic ability was measured by five-fold cross-validation univariate and multi-variate logistic regression. Quality control analyses included volunteer MRI (n=4) and interobserver analysis (n=19). 99 patients were included (50±13yrs, 64 M/35F, 39 IFTA=0, 22 IFTA=2, 20 IFTA=4, 18 IFTA=6, 46 eGFR≤45mL/min/1.73m(2), mean eGFR=47.5±21.3mL/min/1.73m(2)). Spectral diffusion detected fibrosis (IFTA > 0) in patients with normal/stable eGFR > 45ml/min/1.73m(2) [AUC (95% CI)=0.72 (0.56, 0.87), p=0.007]. Spectral diffusion detected mild/ moderate fibrosis (IFTA=2–4) [AUC (95% CI)=0.65 (0.52, 0.71), p=0.023], as did ADC [AUC (95% CI)=0.71 (0.54, 0.87), p=0.013]. eGFR, time-from-transplant, and allograft size could not. Interobserver correlation was ≥0.50 in 24/40 diffusion parameters. Spectral diffusion MRI showed detection of mild/moderate fibrosis and fibrosis before decline in function. It is a promising method to detect early development of fibrosis and CKD before progression
