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Biology subjects

Suter, B.

Publications and source records attributed to Suter, B..

15 recordsLinked to original sources

MECP2 Duplication Uncouples Mitochondrial and Purine Metabolism During neuronal maturation

Mitochondria and nucleotide metabolism are critical for cellular and developmental homeostasis, yet their potential interdependence and role in neurodevelopmental disease remain unclear. In MECP2 Duplication Syndrome (MDS), we identify a conserved correlation between mitochondrial function and purine metabolism that is disrupted across human, organoid, and mouse models. Multiomics integration reveals Complex III as the focal point of mitochondrial collapse, leading to redox stress, DNA damage, and hyperactivation of the de novo purine biosynthesis via purinosome assembly. The breakdown of mitochondria-purinosome coupling compromises genome stability, impairs radial glia proliferation, and delays neuronal maturation. By linking a defined genetic dosage imbalance to metabolic network failure, our study positions the mitochondria-purinosome coordination as a fundamental control axis for neurodevelopment and a therapeutic entry point across metabolic and neurodevelopmental disorders. Metabolic control is fundamental to cellular function, influencing energy production, signaling, epigenetic regulation, and tissue homeostasis1. Nowhere is this more critical than in the brain, where tightly regulated metabolic networks sustain high energetic demands and support neuronal development, synaptic plasticity, and circuit formation2. Disruptions in these networks are increasingly implicated across a spectrum of neurodevelopmental disorders3-5, yet their precise metabolic signatures and mechanistic contributions remain poorly understood.

neuroscience↗

Imp, a key regulator of transposable elements, cell growth, and differentiation genes during embryogenesis

Imps are a highly conserved family of RNA-binding proteins involved in embryonic development, cancer progression, and neurogenesis. However, the molecular pathways and RNAs regulated by Imp to control these processes remain poorly understood. Embryos derived from Imp mutant germline clones arrest development, and transcriptome analysis revealed significant dysregulation of genes involved in cell growth, differentiation, tube morphogenesis, neuronal projection development, and RNA metabolism, along with de-repression of transposable element (TE) RNAs. Consistent with these findings, Imp mutant embryos display TE-overexpression phenotypes, are smaller in size, and exhibit defective organ development, including impaired tracheal branching and gastrulation. Reduced levels of Imp at the larval neuromuscular junction (NMJ) impair synaptic bouton formation and decrease adult longevity. RIP-seq experiments showed that Imp-associated RNAs are enriched for TE RNAs. Proteomic analyses confirmed that several TE-encoded proteins are upregulated in Imp mutant embryos. Specifically, the Ty1 family retrotransposon Copia was derepressed. Consistent with recent findings that Copia is a potent inhibitor of synaptogenesis, its upregulation likely contributes to the impaired NMJ formation and broader embryonic defects observed in Imp mutants. Moreover, Imp associates with piRNA pathway proteins, ensures Piwi nuclear localization, and--like piwi mutants--its loss disrupts TE silencing and causes position-effect variegation (PEV) defects. The analysis of Imp complexes further points to potential mechanisms by which Imp may regulate TE expression. Overall, these results indicate that Imp maintains genome stability and ensures proper developmental progression and neuronal activity by regulating post-transcriptional processes and suppressing transposons.

developmental biology↗

An Augmented Reality Visor for Intraoperative Visualization, Guidance and Temperature Monitoring using Fluorescence

Fluorescence-guided surgical techniques, including tumor resection and tissue soldering, are advancing the frontiers of surgical precision by offering enhanced control that minimizes tissue damage and improves recovery as well as outcomes. However, integrating the visualization of the fluorescent signal and temperature monitoring seamlessly into surgical workflows has not been fully realized and remains a challenge, thus limiting their effectiveness and wide-spread clinical adoption. To address this issue, we introduce an augmented reality (AR) visor designed to unite nanomaterial excitation along with fluorescence detection, and temperature monitoring during surgical procedures. The AR visor was evaluated using advanced fluorescent nanoparticles, such as indocyanine green-doped particles and singlewalled carbon nanotubes. By consolidating fluorescence visualization, excitation monitoring, and precise temperature control into a single AR platform, we equip surgeons with a comprehensive view of both the surgical field and sub-surface conditions invisible to the naked eye. This integration notably improves the safety and efficacy of fluorescence-guided surgeries, as well as emerging technologies including laser tissue soldering, by ensuring the soldering temperature stays within therapeutic thresholds and the laser is accurately guided by real-time fluorescence signals. The presented technology not only enhances existing surgical techniques but also supports the development of new strategies and sensing technologies in areas where traditional methods fall short, marking significant progress in precision surgery, which could ultimately improve patient care.

bioengineering↗

Role of BicDR in bristle shaft construction, tracheal development, and support of BicD functions

Cell polarization requires asymmetric localization of numerous mRNAs, proteins, and organelles. The movement of cargo towards the minus end of microtubules mostly depends on cytoplasmic dynein motors, which function as multiprotein complexes. In the dynein/dynactin/Bicaudal-D (DDB) transport machinery, Bicaudal-D (BicD) links the cargo to the motor. Here we focus on the role of BicD-related (BicDR) and its contribution to microtubule-dependent transport processes. Drosophila BicDR is required for the normal development of bristles and dorsal trunk tracheae. Together with BicD, it contributes to the organization and stability of the actin cytoskeleton in the not-yet-chitinized bristle shaft and the localization of Spn-F and Rab6 at the distal tip. We show that BicDR supports the function of BicD in bristle development and our results suggest that BicDR transports cargo more locally whereas BicD is more responsible for delivering functional cargo over the long distance to the distal tip. We identified the proteins that interact with BicDR and appear to be BicDR cargo in embryonic tissues. For one of them, EF1{gamma}, we showed that EF1{gamma} genetically interacts with BicD and BicDR in the construction of the bristles.

cell biology↗

RNA Targets and Function of Topoisomerase 3β in Reducing Stress inNeuronal Physiology

Topoisomerase 3{beta} (Top3{beta}) works not only on DNA but also RNA. We isolated and identified the naturally cross-linked RNA targets of Drosophila Top3{beta} from an early embryonic stage that contains almost exclusively maternal mRNAs. Favorite targets were longer RNAs, RNAs with many splice sites, and RNAs that become localized in large cells. Demonstrating the importance of its enzymatic activity, Top3{beta} without the hydroxyl group that makes the covalent bond to the RNA, did not allow normal expression and subcellular localization of tested gene products of the identified targets. Top3{beta} is not essential for development to the adult stage but to maintain the morphology of the neuromuscular junction in adult flies and to prevent premature loss of coordinated movement and aging. Alterations in human Top3{beta} have been associated with several neurological diseases and cancers. The homologs of genes and (pre)mRNAs mis-expressed in these conditions show the same characteristics identified in the Drosophila Top3{beta} targets, suggesting that Drosophila could model the function of human Top3{beta}. Indeed, an in vivo test of this model showed that the enzymatic activity of Top3{beta} reduces the neurodegeneration caused by the human (G4C2)49 RNA. Together, these studies show that Top3{beta} plays important roles in normal gene expression, particularly for large genes and long and complex transcripts that need to be transported and translationally controlled. Its absence stresses the cells, seemingly increasing the chances of contracting various neuronal and neurodegenerative diseases and cancers.

cell biology↗

Production of β-PheRS fragments correlates with food avoidance and slow growth, and is suppressed by the appetite-inducing hormone CCHa2

The housekeeping tRNA synthetases play many non-canonical roles with diverse functions. The phenylalanyl-tRNA synthetase (PheRS/FARS) is an 2{beta}2 tetramere. Recently, human patients with mutations in FARSB, the homolog of {beta}-PheRS in Drosophila, have been reported to display problems gaining weight. Here, we show in Drosophila that overexpressing the {beta} subunit in the context of the complete PheRS leads to larval roaming, food avoidance, slow growth, and a developmental delay that can last several days and even prevents pupation. Narrowing down the tissue involved in this behavioral and developmental effect revealed that expression in CCHa2+ and Pros+ cells induced this phenotype. Simultaneous expression of {beta}-PheRS, -PheRS, and the appetite-inducing CCHa2 peptide rescued these phenotypes, linking this {beta}-PheRS activity to the appetite-controlling pathway. The fragmentation dynamics of the excessive {beta}-PheRS points to a {beta}-PheRS fragment as a likely candidate inducer of these phenotypes. Fragmentation of PheRS (FARS) has also been observed in humans and mutations in human {beta}-PheRS (FARSB) can lead to problems in gaining weight. This study, therefore, points to a potential mechanism for the human phenotype and to possible novel approaches to research ways to correct the balance between hunger and satiety signals in the context of obesity.

developmental biology↗

Circular single-stranded DNA is a superior homology-directed repair donor template for efficient genome engineering

The toolbox for genome editing in basic research and therapeutic applications is rapidly expanding. While efficient targeted gene ablation using nuclease editors has been demonstrated from bench to bedside, precise transgene integration remains a technical challenge. AAV6 has been a prevalent donor carrier for homology-directed repair (HDR) mediated genome engineering but has reported safety issues, manufacturing constraints, and restricted applications due to its 4.5 Kb packaging limit. Non-viral targeted genetic knock-ins rely primarily on double-stranded DNA (dsDNA) and linear single-stranded DNA (lssDNA) donors. Both dsDNA and lssDNA have been previously demonstrated to have low efficiency and cytotoxicity. Here, we developed a non-viral genome writing catalyst (GATALYST) system which allows production of ultrapure, minicircle single-stranded DNAs (cssDNAs) up to [~]20 Kb as donor templates for highly efficient precision transgene integration. cssDNA donors enable knock-in efficiency of up to 70% in induced pluripotent stem cells (iPSCs), superior efficiency in multiple clinically relevant primary cell types, and at multiple genomic loci implicated for clinical applications with various nuclease editor systems. When applied to immune cell engineering, cssDNA engineered CAR-T cells exhibit more potent and durable anti-tumor efficacy than those engineered from AAV6 viral vectors. The exceptional precision and efficiency, improved safety, payload flexibility, and scalable manufacturability of cssDNA unlocks the full potential of genome engineering with broad applications in therapeutic development, disease modeling and other research areas. HighlightsO_LIScalable production of minicircle ssDNA (cssDNA) with highly engineered phagemid system C_LIO_LIGenome writing catalyst (GATALYST) system with cssDNA donor template demonstrates superior efficiency and safety in various cell types and genomic loci C_LIO_LIGATALYST gene writing system enables ultra-large transgene integration C_LIO_LIcssDNA engineered CAR-T outperforms AAV engineered CAR-T with superior anti-tumor function C_LI

bioengineering↗

Differential modifications of the C-terminal tails of α-tubulin isoforms and their in vivo importance for kinesin function in Drosophila

Microtubules (MTs) are built from -/{beta}-tubulin dimers and used as tracks by kinesin and dynein motors to transport a variety of cargos, such as mRNAs, proteins, and organelles, within the cell. Tubulins are subjected to several post-translational modifications (PTMs). Glutamylation is one of them, and it is responsible for adding one or more glutamic acid residues as branched peptide chains to the C-terminal tails of both - and {beta}-tubulin. However, very little is known about the specific modifications found on the different tubulin isotypes in vivo and the role of these PTMs in MT transport and other cellular processes in vivo. In this study, we found that in Drosophila ovaries, glutamylation of -tubulin isotypes occurred clearly on the C-terminal ends of Tub84B and Tub84D (Tub84B/D). In contrast, the ovarian -tubulin, Tub67C, is not glutamylated. The C-terminal ends of Tub84B/D are glutamylated at several glutamyl side chains in various combinations. Drosophila TTLL5 is required for the mono- and poly-glutamylation of ovarian Tub84B/D and with this for the proper localization of glutamylated microtubules. Similarly, proper Kinesin-1 distribution in the germline also depends on TTLL5 as well as the refining of Staufen localization and the normal fast ooplasmic streaming with its directional movement, two processes known to depend on Kinesin-1 activities. In the nervous system, the pausing of anterograde axonal transport of mitochondria is affected by an enzymatically dead mutant of TTLL5. Our results demonstrate in vivo roles of TTLL5 in differential glutamylation of -tubulins and point to the in vivo importance of -tubulin glutamylation for Kinesin-1-dependent processes. SummaryO_LI-tubulin glutamylation was established in the C-terminal domain of Drosophila Tub84B and Tub84D (Tub84B/D). Multiple glutamyl residues were pinpointed in this domain. The female germline -tubulin, Tub67C, is, however, not glutamylated. C_LIO_LITTLL5 is required for mono- and poly-glutamylation of Tub84B/D. C_LIO_LITTLL5 is required for the proper Kinesin heavy chain (Khc) distribution in the germline, and the kinesin-based refinement of Staufen localization and ooplasmic streaming during late oogenesis. C_LIO_LITTLL5 is needed for the pausing of anterograde trafficking of mitochondria in axons. C_LI

cell biology↗

Novel roles for BicD in pronuclear fusion and meiosis II progression via localization of the CHC/TACC/Msps complex to MII spindles

Drosophila Clathrin heavy chain (Chc) is transported by the dynein/dynactin microtubule motor through its interaction with the adaptor protein Bicaudal-D (BicD). Here we show that Drosophila BicD and Chc localize to centrosomes and spindles during mitosis and to the tandem spindles during female meiosis II. Reducing the activity of BicD::GFP specifically in freshly laid eggs revealed that BicD is essential for the production of normal female meiosis II products and for pronuclear fusion. Chc interacts with BicD and D-TACC, and BicD is needed to correctly localize the microtubule-stabilizing factors D-TACC, clathrin, and Msps to the meiosis II spindles, suggesting that BicD acts by localizing these proteins. In unfertilized eggs, reduced BicD levels cause the female meiotic products to re-enter the cell cycle. As BicD is required to localize the spindle assembly checkpoint (SAC) components Mad2 and BubR1 to the female meiotic products, it appears that BicD functions to localize them to control metaphase arrest of polar bodies. Finally, Drosophila and C. elegans orthologs of BicD and tacc are also needed for pronuclear fusion.

developmental biology↗

An aminoacylation independent activity of PheRS/FARS promotes growth and proliferation

Summary / AbstractAminoacyl-tRNA synthetases (aaRSs) not only load the appropriate amino acid onto their cognate tRNA, but many of them perform additional functions that are not necessarily related to their canonical activities. Phenylalanyl-tRNA synthetase (PheRS/FARS) levels are elevated in various cancer cells compared to their normal cell counterparts. However, whether and how these levels might contribute to tumor formation was not clear. Here, we show that PheRS is required for cell growth and proliferation. Interestingly, elevated expression of the -PheRS subunit alone stimulates cell growth and proliferation. In the wing discs system, this leads to a strong increase of mitotic cells. Clonal analysis of twin spots in dividing follicle cells revealed that elevated expression of the -PheRS subunit causes cells to grow and proliferate about 25% faster than their normal twin cells. Importantly, this stimulation of growth and proliferation neither required the {beta}-PheRS subunit nor the aminoacylation activity, and it did not visibly stimulate translation. These results, therefore, revealed a non-canonical function of an ancient housekeeping enzyme, providing novel insight into its roles in health and diseases.

cell biology↗

Mms19 promotes spindle microtubule assembly in neural stem cells through two distinct pathways

Mitotic divisions depend on the timely assembly and proper orientation of the mitotic spindle. Malfunctioning of these processes can considerably delay mitosis, thereby compromising tissue growth and homeostasis, and leading to chromosomal instability. Here we identified Mms19 as an important player in these processes as it promotes spindle and astral microtubule (MT) growth and consequently regulates spindle orientation and mitosis duration in Drosophila neural stem cells. Loss of functional Mms19 drastically affects the growth and development of mitotic tissues in Drosophila larvae. We found that Mms19 performs its mitotic activities through two different pathways. By stimulating the mitotic kinase cascade, it triggers the localization of the MT regulatory complex TACC/Msps (Transforming Acidic Coiled Coil/Minispindles, the homolog of human ch-TOG) to the centrosome. In addition, we present evidence that Mms19 stimulates MT stability and bundling by binding directly to MTs.

cell biology↗

Moonlighting α-PheRS connects JAK/STAT with Notch signaling for intestinal homeostasis

The alpha subunit of the cytoplasmic Phenylalanyl tRNA synthetase (-PheRS, FARSA in humans) displays cell growth and proliferation activities and its elevated levels can induce cell fate changes and tumor-like phenotypes that do neither dependent on the canonical function of charging tRNAPhe with phenylalanine nor on stimulating general translation. In intestinal stem cells of Drosophila midguts, -PheRS levels are naturally slightly elevated and human FARSA mRNA levels are elevated in multiple cancers. In the Drosophila midgut model, elevated -PheRS levels caused the accumulation of many additional proliferating cells resembling intestinal stem cells (ISCs) and enteroblasts (EBs). This phenotype resembles partially the tumor-like phenotype described as Notch RNAi phenotype for the same cells. Genetic interactions between -PheRS and Notch suggest that their activities neutralize each other and that elevated -PheRS levels attenuate Notch signaling whether Notch induces differentiation into enterocytes, neuroblast stem cell proliferation, or transcription of a Notch reporter. These non-canonical functions all map to the N-terminal part of -PheRS which accumulates naturally in the intestine. This truncated version of -PheRS (-S) also localizes to nuclei and displays weak sequence similarity to the Notch intracellular domain (NICD), suggesting that -S might compete with the NICD for binding to a common target. Supporting this hypothesis, the tryptophan (W) residue reported to be key for the interaction between the NICD and the Su(H) BTD domain is not only conserved in -PheRS and -S, but also essential for attenuating Notch signaling. Author SummaryAminoacyl tRNA synthetases charge tRNAs with their cognate amino acid to ensure proper decoding of the genetic code during translation. Independent of its aminoacylation function, the alpha subunit of Drosophila cytoplasmic Phenylalanyl tRNA synthetase (-PheRS, FARSA in humans) has an additional activity that promotes growth and proliferation (Ho et al., 2021). Here we describe that elevated -PheRS levels also induce cell fate changes and tumorous phenotypes in Drosophila midguts. Excessive proliferating cells with stem and progenitor cell characteristics accumulate and the composition of the terminally differentiated cells changes, too. This phenotype together with observed genetic interactions between -PheRS and Notch levels show that -PheRS counteracts Notch signaling in many different tissues and developmental stages. This novel activity of -PheRS maps to its N-terminal part, which is naturally produced. The fragment contains a DNA binding domain, translocates into nuclei, and displays essential similarities to a Notch domain that binds to the downstream transcription factor. This suggests that it might be competing with Notch for binding to a common target. Not only because Notch plays important roles in many tumors, but also because FARSA mRNA levels are considerably upregulated in many tumors, this novel activity deserves more attention for cancer research.

cell biology↗

Fast signaling and focal connectivity of PV+ interneurons ensure efficient patternseparation by lateral inhibition in a full-scale dentate gyrus network model

Pattern separation is a fundamental brain computation that converts small differences in synaptic input patterns into large differences in action potential (AP) output patterns. Pattern separation plays a key role in the dentate gyrus, enabling the efficient storage and recall of memories in downstream hippocampal CA3 networks. Several mechanisms for pattern separation have been proposed, including expansion of coding space, sparsification of neuronal activity, and simple thresholding mechanisms. Alternatively, a winner-takes-all mechanism, in which the most excited cells inhibit all less-excited cells by lateral inhibition, might be involved. Although such a mechanism is computationally powerful, it remains unclear whether it operates in biological networks. Here, we develop a full-scale network model of the dentate gyrus, comprised of granule cells (GCs) and parvalbumin+ (PV+) inhibitory interneurons, based on experimentally determined biophysical cellular properties and synaptic connectivity rules. Our results demonstrate that a biologically realistic principal neuron-interneuron (PN-IN) network model is a highly efficient pattern separator. Mechanistic dissection in the model revealed that a winner-takes-all mechanism by lateral inhibition plays a crucial role in pattern separation. Furthermore, both fast signaling properties of PV+ interneurons and focal GC-interneuron connectivity are essential for efficient pattern separation. Thus, PV+ interneurons are not only involved in basic microcircuit functions, but also contribute to higher-order computations in neuronal networks, such as pattern separation.

neuroscience↗

Kinematics associated with treadmill walking in Rett Syndrome

Individuals with Rett syndrome suffer from severely impaired cognitive and motor performance. Current movement-related therapeutic programs often include traditional physical therapy activities and assisted treadmill walking routines for those patients who are ambulatory. However, there are no quantitative reports of kinematic gait parameters obtained during treadmill walking. Here we report the results of an investigation of 17 females diagnosed with typical Rett who walked on a treadmill as speed gradually increased. The objective included characterizing lower limb kinematics, including knee and hip joint range of motions, velocities, limb asymmetries, and the variance associated with these measures. Joint kinematics were obtained using a 12 camera motion capture system and associated processing and analysis software. Stride times progressively decreased as treadmill speeds increased although the range of speeds our participant could walk was quite slow: range 0.2 m/s - 0.5 m/s. There were significant main effects of speed on sagittal knee and hip range of motions and hip velocity. There were large joint asymmetries and variance values relative to both healthy walkers and others patient populations although variance values decreased as walking speed increased. There were significant correlations between joint range of motions and stride times and joint velocities and stride times. The results indicate that Rett patients can adapt their kinematic gait patterns in response to increasing treadmill speed but their ability to do so lies within a narrow range of speeds. We suggest that treadmill training for ambulatory individuals with Rett may further promote improved walking kinematics as well as overall health benefits.

neuroscience↗

NetPyNE: a tool for data-driven multiscale modeling of brain circuits

Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, e.g., a connectivity rule, instead of tens of loops to create millions of cell-to-cell connections. Users can then generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis - connectivity matrices, voltage traces, raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing using NeuroML and SONATA standardized formats. NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate different brain regions and phenomena.

neuroscience↗