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Multiscale simulation and parallel space-time adaptivity of calcium sparks in cardiac myocytes
Full text linkBACKGROUND AND OBJECTIVE: Calcium serves as the bidirectional link between the heart’s electrical excitation and contraction. Electrical excitation induces an influx of Calcium across the sarcolemma and T-tubular membrane, triggering calcium release from the sarcoplasmic reticulum. Calcium sparks, the fundamental events of calcium release from the SR, are initiated in specialized microdomains where Ryanodine Receptors and L-type calcium channels co-locate. The spatial heterogeneity of Calcium release and the random occurrence of strong release fluxes render simulations challenging. Developing mathematical models and efficient simulations of detailed calcium spark models is crucial to understanding heart function. In this paper, we introduce space–time adaptivity within a parallel computing framework into the multiscale simulation of calcium sparks in cardiac myocytes to improve the stability and performance of these simulations. METHODS: We model intracellular calcium concentrations in both the cytoplasm and the SR domains using a set of coupled reaction-diffusion equations. Spatial grid adaptivity is implemented through multilevel finite element methods to account for the spatial heterogeneity of intracellular Ca(2+) release. Rosenbrock-type techniques handle small time steps for simulating stochastic channel opening and closing in the Ca(2+) release units (CRUs). RESULTS: Our test cases demonstrate the superior efficiency of the space-time adaptive approach in optimizing computational resources. The parallel space-time adaptive method accelerates simulations of calcium sparks by a factor of 16.07. CONCLUSIONS: The efficiency and speed gains in Calcium spark simulations are significant and enable modeling based research into previously difficult to tackle questions with regard to sub-micrometer scale models, e.g with respect to local interactions between the Sodium Calcium Exchanger and RyR clusters
Thrombospondin-1 (THBS1) is dysregulated in preeclampsia
Full text linkINTRODUCTION: Preeclampsia involves endothelial dysfunction and impaired angiogenesis. Thrombospondin-1 (THBS1), a pro-thrombotic and anti-angiogenic glycoprotein, may contribute to preeclampsia pathogenesis. This study investigated the role of THBS1 in preeclampsia. METHODS: THBS1 mRNA expression and protein levels were measured in placentas from early-onset preeclampsia (<34 weeks) and gestation-matched controls. Circulating THBS1 was assessed in early-onset preeclampsia and at 36 weeks’ gestation preceding diagnosis of preeclampsia at term. THBS1 was examined during human trophoblast stem cell (hTSC) differentiation into syncytiotrophoblast and extravillous trophoblast (EVT) and compared to a public hTSC organoid dataset. THBS1 regulation was assessed in hTSCs exposed to hypoxia and inflammatory cytokines. Investigating the source of circulating THBS1, we induced endothelial dysfunction in human umbilical vein endothelial cells (HUVECs) with TNFα and treated them with recombinant THBS1. RESULTS: THBS1 mRNA (P < 0.0001, n = 78 vs n = 30 controls) and protein (P = 0.0039, n = 43 and n = 21 controls) levels were significantly reduced in early-onset preeclamptic placentas. Contrastingly, circulating THBS1 was elevated in early-onset preeclampsia (P = 0.011, n = 35 vs n = 27 controls) and preceding term preeclampsia diagnosis (P = 0.0025, n = 21 vs n = 184 controls). THBS1 decreased during syncytiotrophoblast (P = 0.0028) and EVT differentiation (P = 0.0008), indicating mainly cytotrophoblast expression. Analysis of a public hTSC organoid dataset confirmed this. Hypoxic (1 % O2 vs 8 % O2) and TNFα or IL-6 exposure led to differential expression and secretion of THBS1. We observed no changes in THBS1 with induced endothelial dysfunction. Recombinant THBS1 had no effect on endothelial dysfunction. DISCUSSION: THBS1 is dysregulated in preeclampsia and may be regulated by hypoxic stimuli. These findings support THBS1 as a potential mediator in preeclampsia pathogenesis
Supplementation with short-chain fatty acids and a prebiotic improves clinical outcome in Parkinson’s disease: a randomized double-blind prospective study
Full text linkBACKGROUND: Parkinson’s disease is associated with a dysbiotic, proinflammatory gut microbiome, disruptions to intestinal barrier functions, and immunological imbalance. Microbiota-produced short-chain fatty acids, such as propionic and butyric acid promote gut barrier integrity and immune regulation, but their impact on Parkinson’s disease pathology remains mostly unknown. METHODS: In a randomized double-blind prospective study, 72 people with Parkinson’s disease received propionic and butyric acid and/or the prebiotic fiber 2′-fucosyllactose supplementation over 6 months in combination with existing Parkinson’s disease-specific therapy. Patients underwent complete neurological assessment and provided blood and stool samples before as well as 3 and 6 months after supplementation. RESULTS: We observed a robust improvement in motor symptoms, with all intervention groups achieving clinically meaningful reductions. These motor benefits were paralleled by clinically relevant reductions in levodopa medication. In contrast, effects on nonmotor symptoms were more heterogeneous. Notably, the interventions also modulated peripheral immune responses and enhanced mitochondrial respiration in immunocytes. Postintervention microbiota remodeled inflammatory and barrier-related gene sets in gut organ cultures and improved in vitro barrier functions. Treatment response was associated with microbiome composition, distinct patterns of colonic transcription and permeability ex vivo. Multiobjective analysis revealed immune parameters associated with an optimal response to supplementation. CONCLUSION: Short-chain fatty acids ameliorate clinical symptoms in Parkinson’s disease patients and modulate intestinal and peripheral immunity. REGISTRATION: This clinical trial was retrospectively registered with the German Clinical Trials Register (DRKS), registration number DRKS00027061 on 11/19/2021
Molecular plasticity results in oncofetal reprogramming and therapeutic vulnerabilities in juvenile myelomonocytic leukemia
No full textPersistent fetal gene expression in childhood neoplasms is usually explained by a maturation block originating in the prenatal phase. In contrast, reactivation of fetal genes in adult malignancies is considered a consequence of oncofetal reprogramming (OFR) and is associated with aggressive disease. By reconstructing epigenetic ontogeny in juvenile myelomonocytic leukemia (JMML), we identified a postnatal maturation state of JMML stem cells with high transcriptional plasticity indicative of OFR in high-risk disease. Similarly, postnatal activation of oncogenic signaling by inducible Ptpn11E76K mutation in mice triggered molecular plasticity and reactivation of fetal gene expression. Integrative multi-omics analysis revealed aberrant CD52 expression as a feature of high-risk JMML stem cells. Anti-CD52 treatment depleted JMML stem cells and blocked disease propagation in xenograft models. Our results challenge the prevailing maturation block model of pediatric leukemogenesis and establish RAS-associated stem cell plasticity as a determinant of OFR and potential therapeutic vulnerabilities in high-risk JMML. SIGNIFICANCE: Persistent fetal gene expression in pediatric malignancies is considered a consequence of prenatal maturation blockade. In this study, we demonstrate that oncogenic PTPN11 mutations enhance cellular plasticity. This leads to partial restoration of fetal molecular programs, creating new therapeutically exploitable vulnerabilities
Cardiovascular phenotype in women 1-3 years after hypertensive pregnancy disorders: impact of sex-independent and pregnancy-specific risk factors
Full text linkOBJECTIVES: The underlying mechanisms for adversely altered cardiovascular phenotype after hypertensive disorders of pregnancy (HDP) remain poorly understood. We aimed to explore the impact of sex-independent cardiovascular disease (CVD) risk factors on associations between HDP and postpartum echocardiographic findings. STUDY DESIGN: Echocardiography was conducted in 100 women 1-3 years after HDP (n = 65) and normotensive pregnancies according to a standard protocol (n = 35). MAIN OUTCOME MEASURES: Associations between previous HDP and echocardiographic measurements were explored by uni- and multivariate regression analyses. We adjusted for age, body mass index, mean arterial blood pressure and family history of CVD. P-value < 0.05 was considered statistically significant. RESULTS: Women after HDP displayed more adverse cardiometabolic profiles, including more frequent Stage 2 hypertension and less frequent normal blood pressure compared to controls (18 % vs 3 % and 46 % vs 83 %, both p < 0.05). The HDP group had more adverse echocardiographic profiles compared to controls. In univariate regression analyses, HDP was associated with Total Vascular Resistance and Septal Wall diameter. After adjustments for sex-independent cardiovascular risk factors, HDP was significantly associated with Septal Wall diameter in diastole and Relative Wall thickness. CONCLUSIONS: Associations between previous HDP and postpartum echocardiographic findings remained significant after adjustment, but were mostly explained by sex-independent CVD risk factors. Women with previous HDP also displayed more adverse cardiometabolic profiles, including higher hypertension rates. Our findings highlight the need for intensified postpartum CVD prevention in women after HDP. In this cohort, echocardiography provided limited additional information beyond well-known risk factors in the evaluation of CVD risk in asymptomatic women with previous HDP
Fractal dimension of high-risk neuroblastoma vascularity in MRI is associated with chemotherapy response and event-free survival
No full textPURPOSE: To assess therapeutic and prognostic implications of perfusion characterization by fractal analysis using routine MRI in high-risk primary neuroblastomas and to establish a pathophysiologic connection between vascularity phenotype, perfusion imaging characteristics, and treatment response. MATERIALS AND METHODS: In a retrospective cohort study across 30 centers, MRI data of patients with high-risk neuroblastoma (June 2005–February 2021) were collected at the time point of diagnosis (TP1) and after induction chemotherapy before surgery (TP2), with data split into separate discovery (single-center) and validation cohorts (29 centers). Fractal analysis was performed on contrast-enhanced, fat-saturated, T1-weighted sequences at both time points to obtain voxel-wise local fractal dimension (FD) maps for predicting volumetric tumor response. The association of global FD with event-free survival (EFS) was assessed using a Cox proportional hazards model. Additionally, FD was calculated from CD34-stained endothelium in selected histologic tumor samples. Accuracy of response prediction, prognostic value for EFS, and correlation between FD of immunohistochemical vascularity and MRI-derived perfusion were also evaluated. RESULTS: In 73 patients (median age, 3 years [IQR, 3]; 39 male patients; discovery cohort, n = 36; validation cohort, n = 37), local FD maps helped predict volumetric tumor response to induction chemotherapy between TP1 and TP2 with good accuracy (root mean squared error, 47.78 mL; R(2) = 0.94; P < .001), visualizing intratumor high perfusion complexity in areas with low response potential. In multivariate Cox proportional hazards modeling, MYCN status (hazard ratio, 2.30; 95% CI: 1.16, 4.55; P = .017) and global FD at TP2 (hazard ratio, 0.65; 95% CI: 0.47, 0.88; P = .006) were significantly associated with EFS. Complexity of both CD34-immunohistochemical microvascularity (1.23 ± 0.09 [SD] to 1.44 ± 0.07, P < .001) and MRI perfusion (3.40 ± 0.04 to 3.53 ± 0.07, P < .001) increased throughout induction chemotherapy. CONCLUSION: Fractal analysis of MRI-derived perfusion complexity was associated with spatial heterogeneity of chemotherapy response and stratified prognosis in MYCN nonamplified high-risk neuroblastoma, supporting its potential as an imaging biomarker linked to microvascular architecture
An ultrasensitive spatial tissue proteomics workflow exceeding 100 proteomes per day
Full text linkAchieving high-resolution spatial tissue proteomes requires careful balancing and integration of optimized sample processing, chromatography, and MS acquisition. Here, we present an advanced cellenONE protocol for loss-reduced tissue processing and compare all Evosep ONE Whisper Zoom gradients (20, 40, 80, and 120 samples per day), along with three common DIA acquisition schemes on a timsUltra AIP mass spectrometer. We found that tissue type was as important as gradient length and sample amount in determining proteome coverage. Moreover, the benefit of increased tissue sampling was gradient- and dynamic range-dependent. Analyzing mouse liver, a high dynamic range tissue, over tenfold more tissue sampling led to only ∼30% gain in protein identification for short gradients (120 SPD and 80 SPD). However, even the lowest tested tissue amount (0.04 nL) yielded 3,200 reproducibly quantified proteins for the 120 SPD method. Longer gradients (40 SPD and 20 SPD) instead significantly benefited from more tissue sampling, quantifying over 7,500 proteins from 0.5 nL of tonsil T-cell niches. Finally, we applied our workflow to a rare squamous cell carcinoma of the oral cavity, uncovering disease-associated pathways and region-specific protein level changes. Our study demonstrates that more than 100 high-quality spatial tissue proteomes can be prepared and acquired daily, laying a strong foundation for cohort-size spatial tissue proteomics in translational research
Circulating fatty acid binding protein 4 (FABP‐4) concentrations and mortality in individuals with colorectal cancer in the European Prospective Investigation into Cancer and Nutrition study
Full text linkHuman fatty acid binding protein-4 (FABP-4), a protein elevated in obesity that promotes colon cancer cell invasiveness and metastasis, may be associated with higher mortality in individuals with colorectal cancer (CRC) and may serve as a mediator of the obesity–mortality association in these individuals. We used a causal diagram to inform covariate selection and applied Cox proportional hazards models to estimate hazard ratios (HRs) for CRC-specific, non-CRC-specific, and all-cause mortality by FABP-4 levels measured in baseline blood samples from 1371 incident CRC cases from the European Prospective Investigation into Cancer and Nutrition cohort. Competing risk analyses were adapted for CRC and non-CRC deaths. Mediation analyses were conducted to estimate total effects (TEs), direct effects (DEs), and mediation proportions (MPs) by FABP-4 of pre-diagnostic body mass index (BMI) on mortality. In the fully adjusted model including BMI, higher circulating FABP-4 concentrations were associated with higher CRC mortality (HR(Q4vsQ1) = 1.49; 95% CI: 1.11–2.00) and all-cause mortality (HR(Q4vsQ1) = 1.49; 95% CI: 1.15–1.93), but not statistically associated with non-CRC mortality (HR(Q4vsQ1) = 1.51; 95% CI: 0.82–2.76). The TE and DE per 5 kg/m(2) of BMI on all-cause mortality were 1.21; 95% CI: 1.10–1.34, and 1.13; 95% CI: 1.02–1.26, respectively, with a MP of 34.5% (p = .002) by FABP-4. For CRC-specific and non-CRC-specific mortality, MPs by FABP-4 were 33.7% (p = .03) and 36.1% (p = .02), respectively. In conclusion, higher concentrations of FABP-4 were associated with higher CRC-specific and all-cause mortality in individuals with CRC. FABP-4 was a significant partial mediator of the adiposity-mortality relationship in individuals with CRC
Alternative splicing dynamics during human cardiac development in vivo and in vitro
Full text linkCardiomyocytes differentiated in vitro from human induced pluripotent stem cells (iPSC-CMs) are increasingly used in studies of disease mechanisms, drug development, toxicity testing, and regenerative medicine. Alternative splicing (AS) plays a pivotal role in cardiac development. However, the extent to which iPSC-CMs recapitulate native cardiac splicing patterns remains poorly understood. Here, we provide a comprehensive temporal map of AS regulation during human cardiac development. iPSC-derived cardiomyocytes globally recapitulate the transcriptome of prenatal cardiomyocytes, yet their splicing profiles remain heterogeneous, with certain events reflecting early embryonic patterns and others resembling those of later-stage fetal hearts. Moreover, we uncover altered splicing events in iPSC-CMs, including mis-splicing of splicing factors. In conclusion, we present a resource of AS dynamics throughout human cardiac development and a catalog of splicing markers to assess cardiomyocyte maturation in vitro. Our findings provide critical insights into the limitations of iPSC-CM models and their utility in cardiovascular research