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Single-cell multi-omic analysis of mitochondrial mutational mosaicism and dynamics
Full text linkMitochondrial DNA (mtDNA) mutations occur more frequently than nuclear mutations and are associated with various diseases. While single-cell sequencing enables mtDNA variant heteroplasmy analysis, a holistic view of mtDNA mutational landscapes in individual cells has remained limited. Here, we leverage mitochondrial single-cell ATAC-seq and mtDNA-hypermutated POLG(D274A) knock-in HEK293 cell lines to introduce two metrics-single-cell mtDNA mutations per million base pairs (scmtMPM) and heteroplasmy-weighted mitochondrial local constraint scores (scwMSS)-to capture cellular mutational loads and somatic mosaicism. We demonstrate that individual POLG(D274A) cells exhibit complex mutational landscapes, with pathogenic mutations and truncating variants only present at subthreshold levels, indicative of their negative selection. In human healthy donors and mitochondriopathy patients, we identify constrained mutations in complex I, highlighting previously unrecognized mtDNA mutational landscape heterogeneity present on the single-cell level. Overall, scmtMPM and scwMSS provide a framework to investigate fundamental properties of mitochondrial genetics, disease, and somatic mosaicism
BMAL1 modulates glutamine supply to control hematopoietic stem and progenitor cell expansion
Full text linkFollowing specification in the dorsal aorta, hematopoietic stem and progenitor cells (HSPCs) proliferate in the HSPC niche, known as the caudal hematopoietic tissue (CHT) in zebrafish. Here we demonstrate that bmal1a, a core component of the circadian clock machinery, is expressed in CHT endothelial cells (ECs) and affects HSPCs in a non-cell autonomous manner. Using endothelial cell-specific dominant-negative Bmal1a zebrafish lines, we demonstrate a striking increase in HSPC numbers in the CHT, resulting from enhanced HSPC proliferation. RNA-sequencing of dominant-negative bmal1a ECs sorted from the CHT shows a downregulation of glud1a, resulting in increased glutamine levels in the CHT. This newly discovered bmal1a-glud1a-glutamine pathway fuels HSPC expansion. We demonstrate that this glutamine synthesis pathway controlling HSPC expansion is likely conserved in the mouse fetal liver (FL) niche, in which hepatocytes are the likely source of glutamine. Together, our data uncover a novel mechanism of HSPC homeostasis, in which EC BMAL1, expressed by the niche, controls the amount of bioavailable glutamine for HSPCs by regulating the expression of genes involved in glutamine synthesis
Central serous chorioretinopathy occurs in high frequency in myelin oligodendrocyte glycoprotein antibody disease, seropositive and seronegative neuromyelitis optica spectrum disorders compared to multiple sclerosis and healthy controls
No full textBACKGROUND: Neuromyelitis optica spectrum disorders (NMOSD) and myelin oligodendrocyte glycoprotein antibody disease (MOGAD) are autoimmune inflammatory disorders of the central nervous system. Central serous chorioretinopathy (CSCR) is characterized by a serous retinal detachment with leakage of fluid through the retinal pigment epithelium accumulating under the retina. This study investigated a potential association between CSCR and these neuroinflammatory disorders. METHODS: We included people with aquaporin-4 immunoglobulin G (AQP4-IgG) seropositive NMOSD (N = 39), multiple sclerosis (MS, N = 39), myelin oligodendrocyte glycoprotein antibody–associated disease (MOGAD, N = 13), seronegative NMOSD (SN-NMOSD, N = 9), and healthy controls (HC, N = 30). Using optical coherence tomography (OCT), we assessed CSCR frequency and the thickness of the peripapillary retinal nerve fiber layer (pRNFL). RESULTS: There was a higher CSCR frequency (21.3%) throughout all investigated subgroups (AQP4-IgG seropositive NMOSD, MOGAD, and SN-NMOSD) than in the HC group (p = 0.048), with a significant association between CSCR and arterial hypertension frequency but not with these diagnoses, retinal neuroaxonal loss, or history of optic neuritis. CONCLUSION: The high frequency of CSCR suggests a potential benefit of routine monitoring of CSCR in patients with NMOSD and MOGAD using the OCT technology, a reliable method to detect and monitor CSCR in patients with neuroinflammatory disorders. Further research is necessary to establish the underlying pathophysiology and potential effects on vision
Immunomodulatory activity of isolated phenanthrene and dihydrophenanthrene derivatives (coelotrinins A-L) from Coelogyne trinervis
No full textTwelve previously undescribed compounds, named coelotrinins A-L (1-12), comprising eight dihydrophenanthrene derivatives (1, 4-5, and 7-11), two phenanthrene derivatives (2-3), and two phenanthrene-dihydrophenanthrene derivatives (6 and 12), along with 21 known compounds (13-33), were isolated from the pseudobulbs of Coelogyne trinervis. The structures were elucidated via spectroscopic data analysis, and their configurations were determined by optical rotation values and by comparing experimental and calculated electronic circular dichroism curves. Among these compounds, four compounds 1, 16, 23, and 24 showed immunomodulatory effects by inhibiting LPS-induced TNF-α production in THP-1 monocytes. Only coelotrinin A (1) exhibited an immunomodulatory effect with suppression on human peripheral blood mononuclear cells isolated from patients with multiple sclerosis
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Full text linkThe pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands robust quality control and consistent annotation pipelines to ensure meaningful biological insights. proGenomes4 (prokaryotic Genomes v4) addresses this challenge by providing a resource of nearly 2 million high-quality microbial genomes, a doubling in scale from previous versions, encompassing over 7 billion genes. Each genome underwent rigorous quality assessment and comprehensive functional annotation by applying multiple standardized annotation workflows, including the systematic identification of mobile genetic elements and biosynthetic gene clusters. proGenomes4 contains 32 887 species with ecological habitat metadata as well as precomputed pan-genomes. This substantially expanded resource provides the microbiology community with a foundation for large-scale comparative studies and is freely accessible via a newly developed command line interface and at https://progenomes.embl.de/
Serum amyloid A in HFpEF and cardiometabolic diseases
Full text linkHeart failure with preserved ejection fraction (HFpEF) accounts for more than half of all heart failure cases, and its prevalence is projected to rise further. Among its heterogeneous subtypes, cardiometabolic HFpEF, which is driven by metabolic dysfunction, represents a globally predominant form. Recent advances in preclinical models have highlighted metabolic disturbances and systemic inflammation as key contributors to HFpEF pathogenesis. While much attention has focused on classical inflammatory mediators such as interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α), the full spectrum of upstream inflammatory drivers and the therapeutic strategies targeting inflammation in cardiometabolic HFpEF remain incompletely defined. Among emerging candidates, serum amyloid A (SAA) family proteins, highly inducible acute-phase proteins, have attracted growing attention due to their elevated levels in chronic metabolic diseases. Here, we summarize clinical associations between elevated SAA levels and major cardiometabolic conditions—including obesity, diabetes, metabolic dysfunction-associated steatotic liver disease (MASLD, formerly NAFLD), and hypertension—and discuss potential mechanisms based on preclinical studies. We place particular emphasis on the known and potential pathogenetic role of SAA in cardiometabolic HFpEF, where it may contribute to systemic inflammation, endothelial dysfunction, and myocardial fibrosis. Overall, this review aims to advance understanding of SAA in HFpEF and cardiometabolic disease, and to support translational efforts toward improved diagnosis and treatment
An ultrasensitive spatial tissue proteomics workflow exceeding 100 proteomes per day
No full textAchieving 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, 40,000 µm3) 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
Effect of temperature ramp in rapid folding of 3D DNA origami structures
Full text linkDNA origami (DO) has emerged as a powerful technique for constructing nanoscale structures and devices. However, conventional folding protocols for complex 3D DO structures are slow, typically requiring 24 h or longer, limiting scalability for practical applications. Here, we investigate the role of the temperature ramp in DO folding and propose a modified protocol that confines annealing to a 60°C–40°C window. Using four distinct designs, a 20‐helix square box, a 24‐helix bundle, a 13‐helix ring, and a switchable cross structure, we evaluate folding yield, structural uniformity, and functional performance across a range of folding times and buffer conditions. We find that folding occurs rapidly within the 60°C–40°C window, with over 85% of the yield of the conventional 30 h protocol achieved within 1–3 h. Functional switching of the cross structure is retained even in samples folded in 30 min. For aggregation‐prone structures, such as the 13‐ring, the shorter ramp reduces multimer formation and improves the usable yield compared to prolonged folding. These findings confirm the critical influence of the temperature ramp in DO assembly and provide a broadly applicable protocol for faster folding, with potential impact in rapid prototyping, screening, and applications such as plasmonics, sensing, lithography, and metamaterials
Clonal hematopoiesis and lymphoma-associated mutations in hematopoietic progenitors in B-cell non-Hodgkin lymphoma
No full textGene-specific expansion patterns were evident among the most frequent CH lesions, with DNMT3A-mutant clones exhibiting impaired hematopoietic differentiation and TET2-mutant clones showing multi-lineage propagation. Notably, identical CH clones were detected in 41% of corresponding lymphomas, displaying distinct clonal dynamics: tumor-promoting CH (expansion in B-NHL; 10/16 clones; mainly TP53) and tumor-infiltrating CH (no expansion; mainly DNMT3A). Moreover, we identified lymphoma-associated mutations in flow-sorted hematopoietic progenitors from patients with indolent but not aggressive B-NHL and observed a stepwise accumulation of mutations along the lymphoid differentiation path. Single-cell genotyping confirmed the presence of mutated progenitors in 3 follicular, 2 mantle cell and 2 marginal zone lymphoma patients, providing direct evidence of a pre-neoplastic state in disease pathogenesis. Our findings offer novel insight into the cellular origin of nodal B-NHLs and highlight a previously underappreciated role for early clonal events involving the stem/progenitor cell compartment
Cell-autonomous control coupled with tissue context regulates the cessation of migration at the site of organ development
Full text linkOrgan development relies on interactions among different cell types that form three-dimensional structures to carry out specific tasks. This process often involves active migration of progenitor cells toward specific positions within the embryo, where the cells then become immotile and form stable connections among themselves and with neighboring cells. In this work, we study the process of motility loss using zebrafish primordial germ cells as an in vivo model. We show that changes in embryonic tissues as well as cell-autonomous events regulate germ cells' behavior as they arrive at their target region. Importantly, we find that reduction in germ cell motility is correlated with the decay of RNA encoding for Dead end 1 (Dnd1), a conserved vertebrate RNA-binding protein that is essential for PGC migration. Indeed, decreasing or increasing the level of Dnd1 results in a premature or delayed stop to motility, respectively. These findings represent an RNA decay-based mechanism for timing the duration of cell migration in vivo