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Do metabolic fluxes change with age?
Full text linkMetabolomes change with age. Yet, fluxomics points to a contradiction: Jankowski et al. in Cell Metabolism report shifts in metabolite concentrations in aged mice, alongside largely preserved metabolite fluxes, evoking important questions on the nature of age-related metabolic disturbances. We discuss how this might recalibrate our understanding of aging metabolism
Metamaterial antennas enhance MRI of the eye and occipital brain
Full text linkA metamaterial-integrated radio frequency antenna (MTMA), implemented in planar and bend configurations, enables high-resolution MRI of the eye, orbit, and occipital brain at 7.0 T. Its dual-layer co-planar architecture integrates a two-channel transceive loop with a metamaterial layer composed of subwavelength epsilon-negative unit cells. These unit cells were custom-designed based on classical split-ring resonators for operation at 7.0 T. Electromagnetic simulations, including human voxel models, guided the design and characterization of the MTMA's electromagnetic behavior. Both MTMA configurations were benchmarked against conventional loop coil arrays in phantoms and in vivo for experimental validation, demonstrating enhanced transmit (B(1)(+)) efficiency and receive sensitivity enabled by the metamaterial layer through resonant near-field coupling. MRI safety was verified through SAR simulations, bio-thermal modeling, Magnetic Resonance thermometry, and fiber-optic sensors, confirming compliance with safety guidelines. The Bend-MTMA enabled in vivo human MRI of the eye and orbit in healthy volunteers, including B(1)(+) mapping, and provided diagnostic T(1)- and T(2)-weighted imaging in volunteers with retinal pathology and sinus cysts, demonstrating clinical applicability. The Planar-MTMA enabled occipital lobe MRI in human volunteers, achieving superior signal coverage and transmit performance. The modular unit cell design enables tuning across MRI magnetic field strengths, establishing a clinically translatable metamaterial-integrated antenna platform for ocular and neurological imaging
Time‑resolved multi-omic analysis of paclitaxel exposure in human iPSC‑derived sensory neurons unveils mechanisms of chemotherapy‑induced peripheral neuropathy
Full text linkThe microtubule-stabilizing drug paclitaxel remains the standard of care for various solid malignancies but frequently leads to chemotherapy-induced peripheral neuropathy (CIPN). CIPN is a leading cause for premature treatment termination and a significantly reduced quality of life in long-term cancer survivors. The molecular mechanisms of neuro-axonal degeneration, neuroinflammation, and pain in patients treated with paclitaxel remain incompletely understood, and there are currently no predictive biomarkers or preventive treatments. We used human iPSC-derived sensory neurons exposed to paclitaxel to comprehensively model the pathophysiology of CIPN. Neurotoxicity was assessed over time using viability assays and sequential RNA sequencing, as well as deep proteome and lipidomic analyses. We observed a time and dose-dependent decline of cell viability at clinically relevant paclitaxel doses. Sequential RNA sequencing defined JUN as an early immediate gene, followed by the overexpression of genes of the neuronal stress response (e.g., ARID5A, WEE1, DUSP16, GADD45A), neuronal injury and apoptotic pathways (e.g., ATF3, HRK, BBC3 [PUMA], BCL2L11 [BIM], CASP3), neuroinflammation and nociception (CALCB, MMP10, IL31RA, CYSLTR2, C3AR1, TNFRSF12A) and neuronal transduction (e.g., CAMK2A, STOML3, PIRT), while key enzymes of lipid biosynthesis were markedly downregulated (e.g., LSS, HMGCS1, HMGCR, DHCR24). Deep proteome analyses following 48 h of exposure to 100 nM paclitaxel revealed a strong correlation of differentially expressed RNA with proteins, and a marked degradation of essential axonal transport proteins such as kinesins, stathmins, and scaffold proteins. Consistent with the downregulation of rate-limiting enzymes of lipid biosynthesis, lipidome analysis confirmed deregulation of neuronal lipid homeostasis. In summary, paclitaxel induces transcriptomic and proteomic signatures of the neuronal stress response, neuroinflammation, nociception, and disturbed metabolism. These may explain, in part, the clinical phenotype of sensory loss, hypersensitivity, and neuropathic pain frequently observed in patients suffering from CIPN, but constitute pharmacologically addressable targets
Mutated FGFR1 is an oncogenic driver and therapeutic target in high-risk neuroblastoma
No full textFibroblast growth factor receptor 1 (FGFR1) is recurrently mutated at p.N546 in neuroblastoma. We here sought to examine whether mutant FGFR1 is an oncogenic driver, a predictive biomarker, and an actionable vulnerability in this malignancy. FGFR1 mutations at p.N546 were associated with high-risk disease and rapid tumor progression, resulting in dismal outcome of these patients. Ectopic expression of FGFR1(N546K) induced constitutive down-stream signaling and interleukin-3-independent growth in Ba/F3 cells, indicating oncogene addicted proliferation. In FGFR1(N546K);MYCN transgenic mice, neuroblastoma developed within the first days of life with fatal outcome within 3 weeks, reflecting the devastating clinical phenotypes of patients with FGFR1 mutant high-risk neuroblastoma. Treatment with FGFR inhibitors impaired proliferation and pathway activation in FGFR1(N546K)-expressing Ba/F3 and patient-derived FGFR1(N546K) mutant neuroblastoma cells, and inhibited tumor growth in FGFR1(N546K);MYCN transgenic mice and in a chemotherapy-resistant patient-derived xenograft mouse model. In addition, partial regression of FGFR1(N546K) mutant tumor lesions occurred upon treatment with the FGFR inhibitor futibatinib and low-intensity chemotherapy in a patient with refractory neuroblastoma. Together, our data demonstrate that FGFR1(N546K) is a strong oncogenic driver in neuroblastoma that is associated with failure of current standard chemotherapy, and suggest potential clinical benefit of FGFR-directed therapies in FGFR1 mutant high-risk patients
Oculomotor abnormalities in patients with cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) reflect midline cerebellar impairment
Full text linkBACKGROUND: Biallelic intronic repeat expansions in the RFC1 gene are associated with the cerebellar ataxia, neuropathy, and vestibular areflexia (bilateral vestibulopathy) syndrome (CANVAS). Oculomotor abnormalities may serve as a state marker exclusively reflecting the midline cerebellar involvement in CANVAS, i.e., independent of the combined disorders affecting the patient’s postural control stance and gait. METHODS: Slow and fast eye movements of 15 CANVAS patients and 14 healthy subjects were compared using a high-resolution video-based eye tracker allowing to record visually-guided saccades, gaze-holding function and smooth pursuit paradigms. Scores of cognitive impairment were related to oculomotor performance. RESULTS: Saccades (latency, metria, velocity) were normal. Small amplitude omnidirectional gaze-holding deficit was found in 70% of patients, with downbeat nystagmus (60%) being more common than upbeat nystagmus (13%). Latency of initial acceleration of smooth pursuit was prolonged and there was severe impairment of smooth pursuit eye movements. Montreal Cognitive Assessment (MoCA) scores were lower in patients and correlated with saccade and pursuit latency and initial acceleration. Disease duration and vestibulopathy correlated with no oculomotor abnormalities. CONCLUSION: Cerebellar oculomotor dysfunction affected mainly smooth pursuit and gaze holding function at eccentric gaze positions, but it did neither comprise spontaneous nystagmus nor saccade abnormalities. Prolonged latencies in initial pursuit acceleration might be related to the patient’s cognitive decline, but normal saccade latencies point to cerebellar oculomotor neurodegeneration. Smooth pursuit impairment was not related to disease duration and vestibulopathy, contrariwise pursuit impairment became worse with larger functional impairment. Oculomotor abnormalities in CANVAS are in line with midline cerebellar impairment without evidence for extracerebellar (brainstem) brain involvement
Deep immune-phenotyping of HLA-homozygous iPS-cardiomyocytes by spectral flow cytometry
Full text linkINTRODUCTION: Immunogenicity of allogeneic human induced pluripotent stem cell (hiPSC)-derived transplants limits their applicability in regenerative medicine. Selecting human leukocyte antigen (HLA)-homozygous hiPSC lines could be a mitigation strategy and haplo-matching would profoundly expand thenumberof potential recipients. Here we show deep immune-phenotyping of hiPSC-derived cardiomyocytes(iPS-CM)differentiated from four independentiPSClinesinthree centers under chemically defined conditions. METHODS AND RESULTS: Broad immunophenotyping with 354 antibodies revealed differential expression of 101 immune-related molecules between iPS-CM and the parental hiPSC lines. We selected 54 key immune markers for deep immunephenotyping by spectral flow cytometry at the single-cell level. We found that HLA-homozygousiPSCMsexhibit anoverall stable immune-phenotype across HLAhomozygous and heterozygous hiPSC lines indicating a robust differentiation process. HLA-homozygous iPS-CM displayed significantly reduced HLA-ABC levels compared to heterozygous counterparts with an otherwise conserved immune-phenotype. Upon interferon gamma challenge as a surrogate of immune stress responsiveness, iPS-CM significantly upregulated HLA-ABC,-E,-F, PD-L1, PDL2 and the 'don't eat me' signal CD47. As a proof-of-concept we used this panel to benchmark iPS-CM differentiation across three production sites in this study. DISCUSSION: The data indicate generally stable immune-phenotype of iPS-CM produced at three different sites and support feasibility of monitoring iPS-CM identity by spectral flow cytometry
Human ADA2 deficiency is characterized by the absence of an intracellular hypoglycosylated form of adenosine deaminase 2
Full text linkHuman deficiency of adenosine deaminase 2 (DADA2) is an autoinflammatory disease caused by pathogenic variants in ADA2 that lead to impaired deaminase activity. Recently, a lysosomal function of ADA2 has been proposed but an intracellular form of the protein has not yet been characterized. Here, we analyze protein expression of mutant ADA2 in human monocyte-derived macrophages from 10 DADA2 patients. We identify an intracellular low-molecular-weight (LMW) form of ADA2 that undergoes glycan trimming by α-mannosidases and is absent in DADA2 macrophages. Subcellular fractionation and immunofluorescence microscopy demonstrate that LMW-ADA2 is localized in the lysosomes. By overexpression of 34 ADA2 variants in HEK293T and U-937 cells, we show that absence of LMW-ADA2 strongly correlates with reduced deaminase activity and predicts variant pathogenicity. In conclusion, we describe a previously unreported intracellular hypoglycosylated form of ADA2 and establish the absence of this LMW-ADA2 as a cellular characteristic of DADA2. Thereby, we introduce a protein correlate of the recently described lysosomal form of ADA2
Pediatric and adult point of view on the gut-kidney axis in CKD
Full text linkChronic non-communicable diseases pose a significant global health challenge, with the human gut microbiota emerging as a key player in several (patho) physiological functions, including immunity, metabolic homeostasis, and inflammation. While dysbiosis, or imbalance in taxonomy and function of gut microbiota, has been implicated in chronic kidney disease (CKD), whether it is a cause or consequence of the disease remains controversial. Understanding the gut microbiota's role in CKD pathogenesis is essential for developing novel therapeutic interventions. CKD in children presents unique opportunities for studying disease-specific mechanisms due to the absence of comorbidities typically seen in adults, such as diabetes, obesity, and hypertension, although few studies exist. On the other hand, unlike the relatively stable gut microbiota of healthy adults, the infant's microbiome undergoes significant development and maturation during the early years of life. Integrating knowledge from both pediatric and adult populations may provide a comprehensive understanding of gut microbiota dysbiosis in CKD. This review aims to provide an overview of the gut microbiota's development in healthy individuals and CKD patients and discusses how these findings can inform personalized treatment approaches to CKD
SMART v10: three decades of the protein domain annotation resource
Full text linkSMART (Simple Modular Architecture Research Tool, https://smart.embl.de) is a web-based platform for identifying and annotating protein domains and analyzing domain architectures. SMART version 10 features manually curated models for over 1300 protein domains. Approaching its 30th anniversary, SMART’s user interface has been redesigned from the ground up, leveraging modern web technologies to enhance intuitiveness and usability. SMART’s “Genomic” mode, which annotates proteins from completely sequenced genomes was synchronized with the current release of STRING, and now includes 12 035 species, compared to 5090 in the previous release. Protein and domain annotation pages have been updated with new information sources. Integration with eggNOG provides links to 17.5 million orthologous groups for over 53 million proteins. Additionally, synchronization with the interactive Pathways Explorer version 3 incorporates updated KEGG pathway and orthologous group data, enabling direct visualization on four distinct pathway overview maps
The RNA-binding protein Quaking is essential for cardiac homeostasis and function by regulating Morf4l2 splicing
No full textBACKGROUND: Lower levels of Qki were reported in human and mouse-failing hearts, implicating its involvement in cardiac diseases. However, the molecular and functional effects of its downregulation in adult myocardium remain largely unknown. OBJECTIVE: We aim to uncover the effects of Qki knockdown in adult hearts. METHODS & RESULTS: Here we show that AAV9-mediated knockdown of Qki by shRNAs in the hearts of adult BALB/c mice led to cardiac malfunction, atrophy, apoptosis, heart failure, and death within two weeks. Global transcriptomic analysis of Qki knockdown hearts revealed significant dysregulation of 996 alternative splicing events upon Qki knockdown. Mechanistically, we discovered that loss of Qki promotes the exclusion of the third exon of Morf4l2, leading to higher expression of exon three excluded variant (Morf4l2Δex3). Like rodents, the RNA-seq dataset from 108 human hearts revealed a lower splice junction count of MORF4L2 exon three in hearts with low levels of QKI compared to subjects with higher QKI levels. Specific knockdown of Morf4l2Δex3 rescues Qki knockdown-induced cardiac cachexia and improves cardiac function. Moreover, Morf4l2Δex3 was increased in the colon cancer-induced cardiac cachexia mouse model, and its inhibition prevented cardiac cachexia and improved cardiac function. Mechanistically, exon three of Morf4l2 lies in the 5'UTR, and its exclusion leads to higher expression of MORF4L2 upon Qki knockdown due to the lack of a G2-quadruplex. Importantly, MORF4L2 protein sequence and localization were not affected by alternative splicing as exon three lies in the 5'UTR. We found that MORF4L2 is a chromatin-bound protein and regulates H3K27ac. CONCLUSION: Qki knockdown in the adult heart leads to cardiac cachexia due to the alteration of Morf4l2 splicing. Inhibition of Morf4l2Δex3 inhibits cancer-induced cardiac cachexia, demonstrating it as a potential therapeutic target