Biology subjects

Hammerschmidt, M.

Publications and source records attributed to Hammerschmidt, M..

8 recordsLinked to original sources

bioRxiv2025

Exploring mechanisms of scar-free skin wound healing in adult zebrafish in comparison to mouse

Adult zebrafish have the ability to perfectly regenerate their skin after injury without leaving a scar behind. Yet, they intermediately form a collagen-rich granulation tissue that later fully regresses. In contrast, adult mammals lose this ability, resulting in persistent tissue fibrosis and scarring. We performed single-cell RNA sequencing to better characterize the dynamics and heterogeneity of involved cell types during different stages of zebrafish cutaneous wound healing, focusing on macrophages and fibroblasts. Macrophage subclusters display pro- and/or anti-inflammatory/repair characteristics, and fibroblast subclusters characteristics of extracellular matrix formation and degradation, which largely co-exist during all stages of wound healing. Strikingly, some fibroblasts display signatures of myofibroblasts, implicated in fibrotic healing in mammals. In addition, zebrafish fibroblasts express multiple genes with described pro-fibrotic effects in mammalian models. One of them is plod2, which encodes lysylhydroxylase 2. In cutaneous mouse wounds, Plod2 is induced in fibroblasts by macrophage-released Resistin-like molecule RELM encoded by the Retlna gene, promoting the formation of DHLNL collagen crosslinks and thereby less resolvable fibrotic tissue. retln genes are absent from the zebrafish genome; nevertheless, plod2 expression is initiated in zebrafish dermal fibroblasts upon wounding, in this case via TGF{beta} signaling, accompanied by increased collagen DHLNL crosslinking. Yet, both transgenic overexpression and genetic knock-out of plod2 do not interfere with granulation tissue formation and regression, pointing to additional pathways assuring the resolution of transient fibrosis in zebrafish skin wounds even in the presence of strong collagen crosslinking.

developmental biology↗

bioRxiv2025

Rapid replacement of established by exotic genetic lineages of the fungal maize pathogen Exserohilum turcicum in the Swiss Rhine valley

The fungal maize pathogen Exserohilum turcicum, the causative agent of Northern Corn Leaf Blight (NCLB) was introduced to Europe in the late 19th century, E. turcicum where it rapidly expanded. It persisted in four major clonal lineages and multiple physiological races, defined by their interactions with maize disease resistance genes. In a metagenomic survey of natural infections on the susceptible traditional landrace Rheintaler Ribelmais in the Swiss Rhine Valley during 2016 and 2017, we found that one of these clonal lineages ( Small clonal cluster) was dominant in the region. We repeated the surveys in subsequent years and applied a novel pooling strategy to facilitate large-scale sampling by combining ten infected leaves per sampling location. This approach increased sample throughput while reducing sequencing and laboratory costs. The new survey revealed in 2021 and 2022 a significant temporal shift in population structure of exotic genetic lineages from the tropical Kenyan cluster, which have become predominant. It indicates recent introduction and establishment of genetically diverse, tropical E. turcicum lineages into a temperate agricultural system, possibly facilitated by climate change and global seed exchange. Phyllobiome analyses of infected leaves showed that microbial community composition varied across years but remained largely consistent between maize variety types (landrace vs. hybrid). Overall, metagenomic pool sequencing of infected leaves proves to be a cost-effective, spatially resolved method for pathogen monitoring and provides useful evidence for the evolving epidemiology of E. turcicum, with implications for developing durable resistance in maize breeding programs.

plant biology↗

bioRxiv2024

Regional Diversity and Leaf Microbiome Interactions of the Fungal Maize Pathogen Exserohilum turcicum in Switzerland: AMetagenomic Analysis

The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allows to monitor eco-evolutionary dynamics and interactions betwen host, pathogen and the plant microbiome. Exserohilum turcicum, the causal agent of northern corn leaf blight (NCLB) in maize, is distributed in multiple clonal lineages throughout Europe. To characterize regional pathogen diversity, we conducted metagenomic DNA sequencing on 241 infected leaf samples from the highly susceptible Swiss maize landrace Rheintaler Ribelmais, collected over three years (2016-2018) from an average of 14 agricultural farms within the Swiss Rhine Valley. All major European clonal lineages of E. turcicum were identified. Lineages differ by their mating types which indicates potential for sexual recombination and rapid evolution of new pathogen strains, although we found no evidence of recent recombination. The associated eukaryotic and prokaryotic leaf microbiome exhibited variation in taxonomic diversity between years and locations and is likely influenced by local weather conditions. A network analysis revealed distinct clusters of eukaryotic and prokaryotic taxa that correlates with the frequency of E. turcicum sequencing reads, suggesting causal interactions. Notably, the yeast genus Metschnikowia exhibited a strongly negative correlation, supporting its known potential as biological control agent against fungal pathogens. Our findings show that metagenomic sequencing is a useful tool for analyzing the role of environmental factors and potential pathogen-microbiome interactions in shaping pathogen dynamics and evolution, suggesting their potential for effective pathogen management strategies.

plant biology↗

bioRxiv2021

Vertebrate hemicentin-1 interacts physically and genetically with nidogen-2

Hemicentins are large proteins of the extracellular matrix that belong to the fibulin family and play pivotal roles during development and homeostasis of a variety of invertebrate and vertebrate tissues. However, bona fide interaction partners of hemicentins have not been described as yet. Here, applying surface plasmon resonance spectroscopy and co-immunoprecipitation, we identify the basement membrane protein nidogen-2 (NID2) as a binding partner of mouse and zebrafish hemicentin-1 (HMCN1), in line with the formerly described essential role of mouse HMCN1 in basement membrane integrity. We show that HMCN1 binds to the same protein domain of NID2 (G2) as formerly shown for laminins, but with an approximately ten-fold lower affinity and in a competitive manner. Furthermore, immunofluorescence and immunogold labelling revealed that HMCN1/Hmcn1 is localized close to basement membranes and in partial overlap with NID2/Nid2a in different tissues of mouse and zebrafish. Genetic knockout and antisense-mediated knockdown studies in zebrafish further show that loss of Nid2a leads to similar defects in fin fold morphogenesis as the loss of Laminin-5 (Lama5) or Hmcn1. Finally, combined partial loss-of-function studies indicated that nid2a genetically interacts with both hmcn1 and lama5. Together, these findings suggest that despite their mutually exclusive physical binding, hemicentins, nidogens, and laminins tightly cooperate and support each other during formation, maintenance, and function of basement membranes to confer tissue linkage.

developmental biology↗

bioRxiv2021

NAMPT-derived NAD+ fuels PARP1 to promote skin inflammation through parthanatos

Several studies have revealed a correlation between chronic inflammation and NAD+ metabolism but the precise mechanism involved is unknown. Here we report that the genetic and pharmacological inhibition of nicotinamide phosphoribosyltransferase (Nampt), the rate-limiting enzyme in the salvage pathway of NAD+ biosynthesis, reduced oxidative stress, inflammation, and keratinocyte DNA damage, hyperproliferation and cell death in zebrafish models of chronic skin inflammation, while all these effects were reversed by NAD+ supplementation. Similarly, genetic and pharmacological inhibition of poly ADP-ribose (PAR) polymerase 1 (Parp1), overexpression of PAR glycohydrolase, inhibition of apoptosis-inducing factor 1, inhibition of NADPH oxidases and reactive oxygen species (ROS) scavenging, all phenocopied the effects of Nampt inhibition. Pharmacological inhibition of NADPH oxidases/NAMPT/PARP/AIFM1 axis decreased expression of pathology-associated genes in human organotypic 3D skin models of psoriasis. Consistently, an aberrant induction of both NAMPT amounts and PARP activity was observed in lesional skin from psoriasis patients. In conclusion, hyperactivation of PARP1 in response to ROS-induced DNA damage, fueled by NAMPT-derived NAD+, mediates skin inflammation through parthanatos cell death. HighlightsO_LINAMPT inhibition alleviates inflammation in zebrafish and human epidermis organoid models of psoriasis. C_LIO_LINADPH oxidase-derived ROS mediates keratinocyte DNA damage and Parp1 overactivation. C_LIO_LIInhibition of parthanatos cell death phenocopies the effects of NAMPT inhibition in zebrafish and human psoriasis models. C_LIO_LINAMPT and PAR metabolism is altered in psoriasis patients. C_LI

immunology↗

bioRxiv2021

Eya1-dependent homeostasis of morphogenetic territories during collective cell migration

Mutations in the transcriptional co-activator Eya1 cause branchio-oto-renal syndrome (BOR) in humans, and the equivalent conditions in vertebrates. BOR has an incidence of 1/40,000 and is characterized by congenital branchial fistulas, malformations of the inner ear and kidney hypoplasia. Therapeutic interventions for BOR are currently limited to reparative surgery, hearing aids and dialysis. Here we use the mechanosensory lateral line in zebrafish to better understand the role of Eya1 in organogenesis. The lateral line develops from a primordium formed by approximately 150 cells that move together from head to tail of the embryo at a constant velocity. This invariant migration occurs over a trail of Sdf1a chemokine and is controlled by the simultaneous action of two receptors. The CXCR4b is expressed in the front half of the primordium where it acts as a chemokine sensor, whereas the CXCR7b is present in the rear half, serving as a chemokine sink to ensure persistent directionality. We show that the loss of Eya1 strongly reduces the expression of CXCR7b, disrupting the coherent motion of the primordium and leading to lateral-line truncations. We also find evidence of reduced epithelial maturation in primordia lacking Eya1. These findings argue for abnormal collective cell chemotaxis as the origin of organ dysmorphia in BOR.

developmental biology↗

bioRxiv2020

TGS1 controls snRNA 3' end processing, prevents neurodegeneration and ameliorates SMN-dependent neurological phenotypes in vivo

Trimethylguanosine synthase 1 (TGS1) is a highly conserved enzyme that converts the 5 mono-methylguanosine cap of snRNAs to a trimethylguanosine cap. Here, we show that loss of TGS1 in C. elegans, D. melanogaster and D. rerio results in neurological phenotypes similar to those caused by Survival Motor Neuron (SMN) deficiency. Importantly, expression of human TGS1 ameliorates the SMN-dependent neurological phenotypes in both flies and worms, revealing that TGS1 can partly counteract the effects of SMN deficiency. TGS1 loss in HeLa cells leads to the accumulation of immature U2 and U4atac snRNAs with long 3 tails that are often uridylated. snRNAs with defective 3 terminations also accumulate in Drosophila Tgs1 mutants. Consistent with defective snRNA maturation, TGS1 and SMN mutant cells also exhibit partially overlapping transcriptome alterations that include aberrantly spliced and readthrough transcripts. Together, these results identify a neuroprotective function for TGS1 and reinforce the view that defective snRNA maturation affects neuronal viability and function.

genetics↗

bioRxiv2019

The Vertebrate Codex Gene Breaking Protein Trap Library For Genomic Discovery and Disease Modeling Applications

The zebrafish is a powerful model to explore the molecular genetics and expression of the vertebrate genome. The gene break transposon (GBT) is a unique insertional mutagen that reports the expression of the tagged member of the proteome while generating Cre-revertible genetic alleles. This 1000+ locus collection represents novel codex expression data from the illuminated mRFP protein trap, with 36% and 87% of the cloned lines showcasing to our knowledge the first described expression of these genes at day 2 and day 4 of development, respectively. Analyses of 183 molecularly characterized loci indicate a rich mix of genes involved in diverse cellular processes from cell signaling to DNA repair. The mutagenicity of the GBT cassette is very high as assessed using both forward and reverse genetic approaches. Sampling over 150 lines for visible phenotypes after 5dpf shows a similar rate of discovery of embryonic phenotypes as ENU and retroviral mutagenesis. Furthermore, five cloned insertions were in loci with previously described phenotypes; embryos homozygous for each of the corresponding GBT alleles displayed strong loss of function phenotypes comparable to published mutants using other mutagenesis strategies (ryr1b, fras1, tnnt2a, edar and hmcn1). Using molecular assessment after positional cloning, to date nearly all alleles cause at least a 99+% knockdown of the tagged gene. Interestingly, over 35% of the cloned loci represent 68 mutants in zebrafish orthologs of human disease loci, including nervous, cardiovascular, endocrine, digestive, musculoskeletal, immune and integument systems. The GBT protein trapping system enabled the construction of a comprehensive protein codex including novel expression annotation, identifying new functional roles of the vertebrate genome and generating a diverse collection of potential models of human disease.

genomics↗