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Kaslin, J.

Publications and source records attributed to Kaslin, J..

9 recordsLinked to original sources

Observing concurrent subcellular dynamics in large living tissues

An outstanding question in eukaryotic biology is the mechanistic connection between events occurring at (sub)cellular levels (time scales of milliseconds to minutes) to those at the tissue levels (tens of minutes to months). Deciphering such mechanisms requires imaging approaches capable of simultaneously achieving high spatial and temporal resolutions for large samples over long periods of time. Here, we demonstrate Airy beam-based light sheet microscopy of organelles in tens to hundreds of cells in a few hundred micrometre-wide tissue environments. We achieve a typical resolution of 320 nm over 266 x 266 x 100 m3 volumes at a temporal rate of 0.05 Hz, typically with generally used fluorophores such as Green Fluorescent Protein, over extended periods of time that allow tracking of organelle and protein dynamics. We validated our approach across different length and time scales by imaging mitochondria and endosome dynamics in very large fields of view in zebrafish tissue, molecular assemblies of myosin as gastrulation proceeds in Drosophila embryos, 3D mitochondrial streaming in mouse oocytes, pressure-driven motility and protrusions in amoebae, mitochondrial dynamics in cancer spheroids, 5 -colour fast imaging in iBlastoids, and endosomal dynamics in single cells. Through these model systems, we demonstrate the versatility of Airy beam light sheet microscopy to image large tissues at unprecedented high resolution; to capture dynamics in photosensitive, delicate samples; and to screen 3D samples. We anticipate that our Airy beam-based approach will represent a pivotal advance in cellular biology--especially developmental biology--as it provides, for the first time, true subcellular resolution over large imaging volumes with high temporal resolution.

developmental biology↗

Profiling of HeLa nucleoplasmic and nucleolar RNAs by Halo-seq proximity labeling

Subcellular RNA localization is a key regulator of gene expression, but transcriptome wide characterization of RNAs enriched in specific cellular compartments has been hindered by methodological limitations in throughput and spatial resolution. Halo-seq is an RNA proximity-labeling approach that enables the extraction of RNAs located near virtually any Halo-tagged bait protein. However, its broader application has been restricted by the limited availability of the required Halo ligand. Here we present a Halo-seq dataset profiling the nucleoplasmic and nucleolar transcriptomes of HeLa cells. Through experimental and computational validation, we demonstrate that our optimized Halo-seq protocol achieves high spatial specificity, enabling robust mapping of compartment-enriched RNA populations.

molecular biology↗

Ca2+-mediated protein citrullination regulates proliferation in the regenerating and malignant CNS

Unlike most adult mammals, regenerative vertebrates can awaken dormant neural stem cells in response to injury. Understanding how this process is regulated could guide strategies to activate stem cells for tissue repair and limit aberrant proliferation in cancers of the CNS. Here, using zebrafish injury models and high-speed live imaging, we identify hydrodynamically-activated Ca{superscript 2} signalling as a key driver of neural stem cell activation. Local injury-associated changes in CSF flow activate mechanoreceptors at the site of spinal cord lesions, triggering pulsatile Ca{superscript 2} activity and progenitor proliferation. We identify Ca{superscript 2}-regulated peptidylarginine deiminase enzymes (PADs) as key downstream effectors that citrullinate intracellular targets in a Ca{superscript 2}-dependent manner to drive progenitor activation. Finally, we show that PAD inhibitors suppress the growth of aggressive medulloblastoma cells in preclinical laboratory models. Together, these findings uncover a novel mechanism of proliferation control in the vertebrate CNS and highlight the value of regenerative studies for identifying therapeutic targets. Graphical Summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/701650v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@3b7a56org.highwire.dtl.DTLVardef@dcc81forg.highwire.dtl.DTLVardef@d6a208org.highwire.dtl.DTLVardef@127de86_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDamage signals trigger changes in cilia activity and CSF flow to create a transient hydrodynamic niche at the site of spinal cord injuries. C_LIO_LISpecialised CSF-contacting neurons detect altered CSF circulation and initiate a signalling relay that culminates in elevated Ca{superscript 2} activity within dormant neural progenitors. C_LIO_LICa{superscript 2}-activated PAD enzymes link Ca{superscript 2} signalling to cell cycle progression by citrullinating intracellular targets in a Ca{superscript 2}-dependent manner. C_LIO_LIPAD inhibition suppresses medulloblastoma growth in preclinical laboratory models, revealing a conserved regulatory mechanism with translational potential. C_LI

neuroscience↗

dirCLIP profiles variant-specific RNA-protein interactions via nanopore long-read sequencing

RNA binding proteins (RBPs) control gene expression through their activities in essentially all processing steps of coding and noncoding RNAs and are dysregulated in disease. With >95% of human multi-exon genes undergoing alternative splicing, the inability to assign RBP sites to distinct RNA variants fundamentally limits our understanding of RNA regulation. We present dirCLIP, a method combining UV crosslinking and immunoprecipitation (CLIP) with amplification-free direct nanopore long-read sequencing preserving full-length transcripts. dirCLIP employs two complementary strategies: direct RNA sequencing detecting amino acid adduct-induced perturbations in current signals and direct cDNA sequencing capturing binding sites as mutations. Benchmarking dirCLIP with SRSF3 demonstrated >75% concordance with short-read-based data, revealed isoform-selective RNA binding and enabled detection of co-occurring binding sites in single RNA molecules. Application to the noncanonical RBP HMGA1 uncovered new AT-hook mediated RNA variant-specific interactions. dirCLIP fundamentally transforms our ability to interrogate RNA regulation of distinct isoforms and transcript variants with direct implications to disease mechanisms and development of RNA therapeutics.

molecular biology↗

Systems-level investigation of mucopolysaccharidosis IIIA identifies deficient synaptic activity as a key driver of disease progression

Mucopolysaccharidoses are lysosomal storage diseases that collectively represent a major cause of lethal, treatment-refractory childhood dementias 1-7 Clinically-useful interventions are hampered due to an incomplete understanding of their neuropathological origins. Using the zebrafish sgsh model of mucopolysaccharidosis IIIA 8 (MPS IIIA, Sanfilippo syndrome A), we conducted several omics-based analyses, and developed and benchmarked a novel bioinformatic feature classification and ranking model for high-throughput datasets - ExIR - to prioritise important features in the progression of neurological manifestations of the disease. We find that the massive endolysosomal burden resulting from increased lysosomal storage of heparan sulfate and other secondarily accumulating substrates, such as sphingolipids, induces abnormal microtubule organisation and vesicle trafficking in neurons. This results in a gradual impairment of synaptic vesicle localisation at the presynaptic terminal and consequently impaired neuronal activity. Importantly, the endolysosomal phenotype in MPS IIIA zebrafish well-precedes the onset of neural pathology, though the larval MPS IIIA brain was found to be more susceptible to perturbation than wild type siblings. Collectively, these analyses demonstrate the presence of a progressive functional neurodegenerative phenotype underpinning neurological disease in MPS IIIA. Our findings provide direct mechanistic evidence linking the well-described lysosomal storage basis for MPS IIIA to its disproportionately severe neural clinical involvement, enabling development and refinement of future therapeutic interventions for this currently untreatable disorder. HighlightsO_LIMPS IIIA represents one of the most common causes of broadly fatal childhood dementia, but the mechanisms underlying disease progression are poorly understood. C_LIO_LIThe first systems-level analyses of disease state and progression in the CNS of an MPS IIIA animal model were performed. C_LIO_LIExperimental data-based Integrative Ranking (ExIR) was developed to provide unbiased prioritisation and classification of biological data as drivers, biomarkers and mediators of biological processes from high-throughput data at a systems level. C_LIO_LIApplication of ExIR to a transcriptomic and proteomic analyses of a zebrafish model of MPS IIIA implies progressive deficiencies in synaptic activity as a key driver of disease progression correlating with progressive neuronal endolysosomal burden and secondary storage diseases. C_LIO_LIA novel unifying explanation of pathobiology and progression of MPS IIIA facilitates identification of clinically targetable features and may be generalised to other neuronopathic storage disorders. C_LI

neuroscience↗

Early migration of precursor neurons initiates cellular and functional regeneration after spinal cord injury in zebrafish.

Zebrafish have a remarkable capacity to regenerate following spinal cord (SC) injury but the responsible cellular events are not well understood. We used in vivo imaging and genetics to pin-point specific cellular processes controlling SC regeneration in zebrafish. We identified two temporally and mechanistically distinct phases of cellular regeneration in the SC. The initial phase relies on migration of precursor neurons to the injury, enabling rapid functional recovery, and activation of quiescent neural progenitor cells (NPCs). A second phase of regenerative neurogenesis compensates for both the lost tissue and cells depleted due to precursor neuron migration. We propose a critical role of precursor neurons recruitment in initiating neuronal circuit recovery and buying sufficient time for regenerative neurogenesis to take place. Taken together, our data suggests an unanticipated role of precursor cell recruitment in driving neural repair and functional recovery during the regenerative response. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/539940v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@12c5be9org.highwire.dtl.DTLVardef@1461e99org.highwire.dtl.DTLVardef@82d28aorg.highwire.dtl.DTLVardef@cc6870_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

Tectal stem cells display diverse regenerative capacities

How diverse adult stem and progenitor populations regenerate tissue following damage to the CNS remains unknown across most neurogenic domains. To understand the role of quiescent radial-glial (qRG) stem cells during regeneration, we tested the hypothesis that qRG could be induced to proliferate and produce newborn neurons. We designed a stab lesion assay in the midbrain tectum of the adult zebrafish to target an isolated population of qRG, and investigated their proliferative behaviour, differentiation potential, and requirement of Wnt/{beta}-catenin signalling for the regenerative response. EdU-labelling showed that a small proportion of qRG transit to a proliferative state (pRG), but that progeny of pRG are restricted to a radial-glial fate. Lesion promoted upregulation of proliferation and neurogenesis from neuro-epithelial-like amplifying progenitors (NE-Ap) of the tectal marginal zone (TMZ). Homeostatic levels of Wnt/{beta}-catenin signalling persisted under lesioned conditions in the qRG/pRG population, whereby increased {beta}-catenin staining and axin2 expression was present in the NE-Ap progenitor zone. Attenuation of Wnt signalling using Dickkopf-1, demonstrated that proliferative responses post-injury appeared to be Wnt-independent. Our results align with the emerging view that adult stem/progenitor phenotypes are characterized by discrete, rather than mutual, regenerative programs and that different stem cell domains employ different modes of regeneration.

neuroscience↗

Accelerated brain aging towards transcriptional inversion in a zebrafish model of familial Alzheimer’s disease

Alzheimers disease (AD) develops silently over decades. We cannot easily access and analyse pre-symptomatic brains, so the earliest molecular changes that initiate AD remain unclear. Previously, we demonstrated that the genes mutated in early-onset, dominantly-inherited familial forms of AD (fAD) are evolving particularly rapidly in mice and rats. Fortunately, some non-mammalian vertebrates such as the zebrafish preserve fAD-relevant transcript isoforms of the PRESENILIN (PSEN1 and PSEN2) genes that these rodents have lost. Zebrafish are powerful vertebrate genetic models for many human diseases, but no genetic model of fAD in zebrafish currently exists. We edited the zebrafish genome to model the unique, protein-truncating fAD mutation of human PSEN2, K115fs. Analysing the brain transcriptome and proteome of young (6-month-old) and aged, infertile (24-month-old) wild type and heterozygous fAD-like mutant female sibling zebrafish supports accelerated brain aging and increased glucocorticoid signalling in young fAD-like fish, leading to a transcriptional inversion into glucocorticoid resistance and vast changes in biological pathways in aged, infertile fAD-like fish. Notably, one of these changes involving microglia-associated immune responses regulated by the ETS transcription factor family is preserved between our zebrafish fAD model and human early-onset AD. Importantly, these changes occur before obvious histopathology and likely in the absence of A{beta}. Our results support the contributions of early metabolic and oxidative stresses to immune and stress responses favouring AD pathogenesis and highlight the value of our fAD-like zebrafish genetic model for elucidating early changes in the brain that promote AD pathogenesis. The success of our approach has important implications for future modelling of AD.

bioinformatics↗

Loss Of lrrk2 Impairs Cell Proliferation And Neuronal Regeneration In The Zebrafish Brain

LRRK2 mutations are a major cause of Parkinsons disease. Pathogenicity of LRRK2 loss-of-function is controversial, as knockout in rodents reportedly induces no brain-specific effects and knockdown studies in zebrafish are conflicting. Here we show that CRISPR/Cas9-engineered deletion of the ~60-kbp-long zebrafish lrrk2 locus elicits a pleomorphic, albeit transient brain phenotype in maternal-zygotic mutants (mzLrrk2). Intriguingly, 11-month-old mzLrrk2 adults display increased dopamine and serotonin catabolism. Additionally, we find decreased mitosis in the larval brain and reduced stab injury-induced neuronal regeneration in the adult telencephalon. Finally, hypokinesia associates with loss of lrrk2 in larvae. Our results demonstrate that lrrk2 knockout has an early neurodevelopmental effect, and leads to perturbed dopamine and serotonin catabolism in a LRRK2 knockout. We propose mzLrrk2 zebrafish as a valuable tool to study LRRK2 loss-of-function in vivo, and provide a link between LRRK2 and the control of basal cell proliferation in the brain that may become potentially critical upon challenges like brain injury.

neuroscience↗