Biology subjects

van Ham, T. J.

Publications and source records attributed to van Ham, T. J..

7 recordsLinked to original sources

bioRxiv2025

TFEB-depletion rescues TMEM106B-related myelin defects in zebrafish

Lysosomal transmembrane protein TMEM106B is genetically and neuropathologically implicated in a range of neurodegenerative diseases. Unexpectedly, the recurrent de novo TMEM106B variant p.(Asp252Asn) causes a hypomyelinating disorder. TMEM106B controls lysosomal positioning in neurons, but its role in white matter health is not fully understood. To study the role of TMEM106B in myelination in vivo, we mutated zebrafish tmem106ba and tmem106bb homologs. In vivo brain imaging in larvae deficient for both homologs (tmem106bdm) showed more, smaller lysosomes, accompanied by reduced myelin content and shorter myelin sheaths. Oligodendrocytes in tmem106bdm exhibited more lysosomes in the perinuclear region. We next genome-edited the pathogenic p.(Asp252Asn) variant into the zebrafish genome and showed that it acts dominant-negatively on myelination and on lysosomal clustering around the nucleus in oligodendrocytes. As lysosomal peri-nuclear positioning modulates mTOR-signaling, and downstream transcription factor EB (TFEB) inhibits myelination, we next investigated whether there is a genetic interaction between TMEM106B and TFEB. Indeed, deficient myelination in tmem106bdm larvae, but not altered lysosomal clustering, was restored by loss of Tfeb in triple mutant larvae. Our work elucidates that TMEM106B modulates myelination by a TFEB-dependent pathway. This implicates the TFEB pathway in myelin development and white matter health and suggests that modulating TFEB could be a therapeutic target in white matter disorders.

genetics↗

bioRxiv2024

The non-canonical thioreductase TMX2 is essential for neuronal survival during embryonic brain development

Biallelic variants in thioredoxin-related transmembrane 2 protein (TMX2) can cause a brain malformation of cortical development (MCD), characterized by primary microcephaly, polymicrogyria and pachygyria by an unknown mechanism. To better understand and visualize how TMX2 loss disrupts brain development in vivo we investigated the function of TMX2, using the zebrafish embryo as a model system. We generated zebrafish deficient for TMX2 ortholog tmx2b, which during the first 2 days post fertilization (dpf) showed normal behavioral activity and brain developmental hallmarks. From 3 dpf onwards however, tmx2b mutants failed to exhibit locomotor activity, which was accompanied by cell death primarily in the brain, but not in other organs or in the spinal cord. Strikingly, cell death in tmx2b mutants occurs specifically in newborn neurons within a [~]1.5-hour timeframe, whereas neuronal progenitor and other glial cells are preserved, and could be suppressed by inhibiting neuronal activity. In vivo GCaMP6s calcium imaging showed a persistent [~]2-fold increase in calcium in neurons after the onset of cell death. This suggests that calcium homeostasis underlies the tmx2b mutant brain phenotype. Altogether, our results indicate that TMX2 is an evolutionary conserved, protective regulator essential specifically for newborn neurons to survive after their differentiation in the vertebrate embryonic brain.

developmental biology↗

bioRxiv2021

Colony stimulating factor 1 signaling regulates myeloid fates in zebrafish via distinct action of its receptors and ligands

Macrophage colony-stimulating factor receptor (M-CSFR/CSF1R) signaling is crucial for the differentiation, proliferation, and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases, including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore, it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human-related diseases. Here, we investigate the roles of zebrafish Csf1rs and their ligands - Csf1a, Csf1b and Il34, in embryonic and adult myelopoiesis. The proliferative effect of exogenous Csf1a on embryonic macrophages is connected to both receptors as it is diminished in both csf1ra{Delta}5bp and csf1rb{Delta}4bp mutants. There is no evident effect of Csf1b in zebrafish embryonic myelopoiesis. Further, we uncover an unknown role of Csf1rb in zebrafish granulopoiesis. Deregulation of Csf1rb signaling leads to failure in myeloid differentiation resulting in neutropenia throughout the whole lifespan. Surprisingly, Il34 signaling through Csf1rb seems to be of high importance as both csf1rb{Delta}4bp and il34{Delta}5bp deficient zebrafish larvae lack granulocytes. Our single-cell RNA sequencing analysis of adult whole kidney marrow (WKM) hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non-overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease, mostly in cancerogenesis. Key pointsO_LIcsf1ra and csf1rb are indispensable for macrophage differentiation and together with csf1a regulate embryonic macrophage fates in zebrafish C_LIO_LIcsf1rb is important for granulocyte differentiation and migration and together with il34 it regulates embryonic granulocytic fates in zebrafish C_LI

developmental biology↗

bioRxiv2021

Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance

BackgroundNon-coding regulatory elements (NCREs), such as enhancers, play a crucial role in gene regulation and genetic aberrations in NCREs can lead to human disease, including brain disorders. The human brain is complex and can be affected by numerous disorders; many of these are caused by genetic changes, but a multitude remain currently unexplained. Understanding NCREs acting during brain development has the potential to shed light on previously unrecognised genetic causes of human brain disease. Despite immense community-wide efforts to understand the role of the non-coding genome and NCREs, annotating functional NCREs remains challenging. ResultsHere we performed an integrative computational analysis of virtually all currently available epigenome data sets related to human fetal brain. Our in-depth analysis unravels 39,709 differentially active enhancers (DAEs) that show dynamic epigenomic rearrangement during early stages of human brain development, indicating likely biological function. Many of these DAEs are linked to clinically relevant genes, and functional validation of selected DAEs in cell models and zebrafish confirms their role in gene regulation. Compared to enhancers without dynamic epigenomic rearrangement, these regions are subjected to higher sequence constraints in humans, have distinct sequence characteristics and are bound by a distinct transcription factor landscape. DAEs are enriched for GWAS loci for brain related traits and for genetic variation found in individuals with neurodevelopmental disorders, including autism. ConclusionOur compendium of high-confidence enhancers will assist in deciphering the mechanism behind developmental genetics of the human brain and will be relevant to uncover missing heritability in human genetic brain disorders.

genomics↗

bioRxiv2021

Myelin biogenesis is associated with pathological ultrastructure that is resolved by microglia during development

To enable rapid propagation of action potentials, axons are ensheathed by myelin, a multilayered insulating membrane formed by oligodendrocytes. Most of the myelin is generated early in development, in a process thought to be error-free, resulting in the generation of long-lasting stable membrane structures. Here, we explored structural and dynamic changes in CNS myelin during development by combining ultrastructural analysis of mouse optic nerves by serial block face scanning electron microscopy and confocal time-lapse imaging in the zebrafish spinal cord. We found that myelin undergoes extensive ultrastructural changes during early postnatal development. Myelin degeneration profiles were engulfed and phagocytosed by microglia in a phosphatidylserine-dependent manner. In contrast, retractions of entire myelin sheaths occurred independently of microglia and involved uptake of myelin by the oligodendrocyte itself. Our findings show that the generation of myelin early in development is an inaccurate process associated with aberrant ultrastructural features that requires substantial refinement.

neuroscience↗

bioRxiv2020

Zebrafish macrophage developmental arrest underlies depletion of microglia and reveals Csf1r-independent metaphocytes

Macrophages derive from multiple sources of hematopoietic progenitors. Most macrophages require colony-stimulating factor 1 receptor (CSF1R), but some macrophages persist in the absence of CSF1R. Here, we analyzed mpeg1:GFP-expressing macrophages in csf1r-deficient zebrafish and report that embryonic macrophages emerge followed by their developmental arrest. In larvae, mpeg1+ cell numbers then increased showing two distinct types in the skin: branched, putative Langerhans cells, and amoeboid cells. In contrast, although numbers also increased in csf1r-mutants, exclusively amoeboid mpeg1+ cells were present, which we showed by genetic lineage tracing to have a non-hematopoietic origin. They expressed macrophage-associated genes, but also showed decreased phagocytic gene expression and increased epithelial-associated gene expression, characteristic of metaphocytes, recently discovered ectoderm-derived cells. We further demonstrated that juvenile csf1r-deficient zebrafish exhibit systemic macrophage depletion. Thus, Csf1r deficiency disrupts embryonic to adult macrophage development. Csf1r-deficient zebrafish are viable and permit analyzing the consequences of macrophage loss throughout life.

developmental biology↗

bioRxiv2018

Reverse genetic screen reveals that Il34 facilitates yolk sac macrophage distribution and seeding of the brain

Microglia are brain resident macrophages, which have specialized functions important in brain development and in disease. They colonize the brain in early embryonic stages, but few factors that drive the migration of yolk sac macrophages into the embryonic brain, or regulate their acquisition of specialized properties are currently known.\n\nHere, we present a CRISPR/Cas9-based in vivo reverse genetic screening pipeline to identify new regulators important for microglia development using zebrafish. Zebrafish larvae are particularly suitable due to their external development, transparency, high fecundity and conserved microglia features. We targeted putative microglia regulators, including signature genes and non-cell autonomous factors, by Cas9/gRNA-complex injections, followed by neutral red-based visualization of microglia. Microglia were quantified automatically in 3-day-old larvae using a software tool we called SpotNGlia. We identified that loss of function of the zebrafish homolog of the colony stimulating factor 1 receptor (CSF1R) ligand IL34, caused strongly reduced microglia numbers in early development. Previous studies on the role of the IL34 on microglia development in vivo were ambiguous. Our data, and a concurrent paper, show that in zebrafish, il34 is required during the earliest seeding of the brain by microglia progenitors. Our data also indicate that Il34 is required for distribution to other organs.\n\nPreviously, we showed that csf1ra and csf1rb double mutant zebrafish have no microglia. As there is a moderate effect of il34 on microglia development, relative to the effect csf1r, additional Csf1r-dependent signalling may be needed for establishment of the microglia network. In all, we identified il34 as a modifier of microglia colonization, by affecting distribution of yolk sac macrophages to target organs, validating our reverse genetic screening pipeline in zebrafish which can be used for the identification of additional regulators of microglia development.

developmental biology↗