Biology subjects

Hofmann, R.

Publications and source records attributed to Hofmann, R..

9 recordsLinked to original sources

bioRxiv2026

Aggrecan hypomorphism accelerates the progression of post-traumatic osteoarthritis in mice

ObjectiveThe Agc1CreERT2 mouse line is a powerful tamoxifen-inducible genetic tool used for conditional gene manipulation specifically in cartilage. The aim of this study was to investigate the effects of aggrecan hypomorphism on the progression of post-traumatic osteoarthritis (PT-OA) in Agc1CreERT2 mice. MethodsProteoglycan content in cartilage samples from the knees of E18.5 embryos were quantified by sulfated glycosaminoglycan (sGAG) assay. Destabilization of the medial meniscus (DMM) surgery was performed to induce PT-OA in 12-week-old wild-type, heterozygous Agc1CreERT2/+ and homozygous Agc1CreERT2/CreERT2 mice. Progression of OA was assessed at 4-, 8-, and 12-weeks post-DMM by OARSI, synovitis and osteophyte maturation histopathology scores and micro-computed tomography ({micro}CT). Aggrecan deposition, cartilage matrix-degrading proteases, aggrecan and collagen II degradation neoepitopes were investigated by immunohistochemical staining, and serum C-terminal cross-linked telopeptide of type II collagen (CTX-II) levels by an enzyme-linked immunosorbent assay (ELISA). Chondrocyte apoptosis was analyzed with the terminal deoxynucleotidyl transferase (TdT) dUTP nick-end labeling (TUNEL) assay. The biomechanical properties of articular cartilage (AC) were investigated with indentation-type atomic force microscopy (IT-AFM). ResultsBefore DMM, homozygous Agc1CreERT2/CreERT2 mice had reduced sGAG and aggrecan levels and increased cartilage stiffness. After DMM, they exhibited increased cartilage degradation, synovitis, osteophyte formation and meniscus mineralization, chondrocyte apoptosis and cartilage stiffness compared with wild-type mice. Immunohistochemistry demonstrated increased expression of the aggrecanase ADAMTS-5, the metalloproteinase MMP-13, the aggrecan degradation neoepitope NITEGE and the collagen degradation neoepitope C1,2C in AC. ELISA also revealed elevated serum CTX-II levels. Heterozygous Agc1CreERT2/+ mice also exhibited accelerated PT-OA compared with wild-type mice, characterized by elevated CTX-II levels at 4-weeks, increased synovitis, osteophyte and soft tissue mineralization at 8-weeks, and more severe cartilage degeneration at 12-weeks post-DMM. ConclusionBoth homozygous and heterozygous Agc1CreERT2mice exhibit increased susceptibility to PT-OA, underscoring the importance of physiological aggrecan expression in maintaining joint homeostasis and regulating joint pathophysiology. These findings indicate that Agc1CreERT2/+mice are not phenotypically neutral in the DMM model and that this intrinsic susceptibility should be considered when interpreting studies employing inducible, cartilage-specific gene deletion.

molecular biology↗

bioRxiv2025

Proximity determines donor candidacy during DNA double-stranded break homology directed repair

DNA double-stranded breaks (DSBs) are especially toxic events that can be reversed by homology-directed repair (HDR), wherein information is copied from an intact template molecule. RAD51 mediates initial DSB/template pairing during homology search. A major challenge in understanding homology search in cells is the lack of tools to monitor this process. We developed RAD51 proximity identification sequencing (RaPID-seq), a sensitive method that marks all candidate templates searched by RAD51. We find that HDR is hierarchical, such that DSB proximity determines template candidacy and subsequent recombination is unlocked by DSB/template homology. Sequences that lie outside the proximal window are not efficiently searched, even if identical in sequence. Our data reveal the invisible process of homology search and shed new light on fundamental mechanisms underlying genome editing.

molecular biology↗

bioRxiv2024

Deep mutational scanning identifies variants of Cas1 and Cas2 that increase spacer acquisition in type II-A CRISPR-Cas systems

A remarkable feature of CRISPR-Cas systems is their ability to acquire short sequences from invading viruses to create a molecular record of infection. These sequences, known as spacers, are inserted into the CRISPR locus by the Cas1-Cas2 integrase complex and mediate sequence- specific immunity in prokaryotes. Spacer acquisition has been used to develop unique biotechnological applications such as the immunization of industrially relevant bacteria against bacteriophage infection and the recording of biological signals into stable genetic information. These technologies, however, are constrained by the low efficiency of the spacer acquisition process. To overcome this limitation, we developed a genetic system that combined deep mutational scanning (DMS) of cas genes from the Streptococcus pyogenes type II-A CRISPR- Cas system with a method that selects bacteria that acquire new spacers. This procedure enabled the identification of cas mutations that support up to a sevenfold increase in the levels of spacer acquisition and a significant enhancement of immunity against phage infection. In addition, our analysis revealed key interactions at the Cas1-Cas2 interface critical for spacer integration. Our findings provide insights into the molecular determinants of spacer acquisition and offer a platform to improve CRISPR-Cas-based applications.

microbiology↗

bioRxiv2023

Life and death in Trypillia times: Interdisciplinary analyses of the exceptional human remains from the settlement of Kosenivka, Ukraine (3700-3600 BCE)

We present an interdisciplinary analysis of finds from the Trypillia settlement of Kosenivka, Ukraine (ca. 3700-3600 BCE, Trypillia C1), that links information on human, faunal, and botanical remains with archaeological data to provide exceptionally detailed insights into life and death at a Trypillia mega-site. We obtained osteological, palaeopathological, and histotaphonomic data from human bone fragments; performed carbon and nitrogen stable isotopic analysis of human and animal bone to calculate food webs with the software FRUITS; and modelled newly generated radiocarbon dates to refine the sites chronology. The biological profile of seven identified individuals, some of whom suffered from disease symptoms common in the Chalcolithic, represents a demographic cross-section of the population. The analysis of perimortem cranial trauma suffered by two individuals suggest cases of interpersonal conflict. Food web calculations demonstrate the large contribution of cereals to the protein component of the human diet, which is supported by dental observations, and we suggest that livestock were a major manure producer for crop cultivation. The most probable scenario for the formation of the Kosenivka find assemblage is a deathly fire event. This makes the site a rare example where the archaeological and osteological results can be used to reconstruct a minimum number of house inhabitants. Following a literature review, we contextualise our analysis by discussing the general lack of human remains from Early and Middle Trypillia sites. The individuals from Kosenivka form part of the less than 0.05% of the total estimated Trypillia population that is represented skeletally; its members were deposited within settlements in the Middle Trypillia stage (until C1), preceding the shift to extramural burials in its late phase (C2). Our detailed results indicate the huge explanatory potential that has yet to be unlocked in the rare and often poorly preserved bioarchaeological archives of the Cucuteni-Trypillia phenomenon.

evolutionary biology↗

bioRxiv2023

C-terminal amides mark proteins for degradation via SCF/FBXO31

During normal cellular homeostasis unfolded and mis-localized proteins are recognized and removed, preventing the build-up of toxic byproducts1. When protein homeostasis is perturbed during aging, neurodegeneration or cellular stress, proteins can accumulate several forms of chemical damage through reactive metabolites2, 3. Such modifications have been proposed to trigger the selective removal of chemically marked proteins3-6; however, discovering modifications sufficient to induce protein degradation has remained challenging. Using a semi-synthetic chemical biology approach coupled to cellular assays, we found that C-terminal amide-bearing proteins (CTAPs) are rapidly cleared from human cells. A CRISPR screen identified the SCF/FBXO31 ubiquitin ligase as a reader of C-terminal amides, which ubiquitylates CTAPs for subsequent proteasomal degradation. A conserved binding pocket enables FBXO31 to bind almost any C-terminal peptide bearing an amide while retaining exquisite selectivity over non-modified clients. This mechanism facilitates binding and turnover of endogenous CTAPs that are formed following oxidative stress. A dominant human mutation found in neurodevelopmental disorders switches CTAP recognition, such that non-amidated neosubstrates are now degraded and FBXO31 becomes markedly toxic. We propose that CTAPs may represent the vanguard of a largely unexplored class of modified amino acid degrons that could provide a general strategy for selective yet broad surveillance of chemically damaged proteins.

cell biology↗

bioRxiv2022

Highlighter: an optogenetic actuator for light-mediated, high resolution gene expression control in plants

Optogenetic actuators have revolutionized the resolution at which we can assert control over biological processes in living systems. In plants, deployment of optogenetics is challenging due to the need for these light-responsive systems to maintain a single activation state in conventional horticultural environments with light-dark cycling. Furthermore, many available optogenetic actuators are based on plant photoreceptors that might crosstalk with endogenous signaling processes, while others depend on exogenously supplied cofactors. To overcome such challenges, we have developed Highlighter; a synthetic, light-gated gene expression system tailored for in planta function. Highlighter is based on the photoswitchable CcaS-CcaR system from cyanobacteria and is repurposed for plants as a fully genetically encoded system, engineered to photoswitch with the endogenous plant chromophore, phytochromobilin. We deployed Highlighter in transiently transformed Nicotiana benthamiana for optogenetic control of fluorescent protein expression and innate immune responses. Using light to guide differential fluorescent protein expression in nuclei of neighboring cells, we demonstrate unprecedented spatiotemporal control of target gene expression. We furthermore regulate activation of plant immunity by modulating the spectral composition of white light, demonstrating optogenetic control of a biological process in horticultural light environments. Highlighter is a step forward for optogenetics in plants and a technology for high-resolution gene induction that will advance fundamental plant biology and provide new opportunities for crop improvement.

synthetic biology↗

bioRxiv2021

Phenotyping in the era of genomics: MaTrics a digital character matrix to document mammalian phenotypic traits coded numerically

A new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) is presented in a digital form. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics. MaTrics was developed as part of a project to link phenotypic differences between mammals to differences in their genomes using Forward Genomics. Apart from genomes this approach requires information on homologous phenotypes that are numerically encoded (presence-absence; multistate character coding*) in a matrix. MaTrics provides these data, links them to at least one reference (e.g., literature, photographs, histological sections, CT-scans, or museum specimens) and makes them available in a machine actionable NEXUS-format. By making the data computer readable, MatTrics opens a new way for digitizing collections. Currently, MaTrics covers 147 mammalian species and includes 207 characters referring to structure, morphology, physiology, ecology and ethology. Researching these traits revealed substantial knowledge gaps, highlighting the need for substantial phenotyping efforts in the genomic era. Using the trait information documented in MaTrics, previous Forward Genomics screens identified changes in genes that are associated with various phenotypes, ranging from fully-aquatic lifestyle to dietary specializations. These results motivate the continuous expansion of phenotype information, both by filling research gaps or by adding additional taxa and traits. MaTrics is digitally available online within the data repository Morph{middle dot}D{middle dot}Base (www.morphdbase.de).

zoology↗

bioRxiv2020

Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks

Delineating the molecular nanoscale organization of the surfaceome is pre-requisite for understanding cellular signaling. Technologies for mapping the spatial relationships of cell surface receptors and their extracellular signaling synapses would open up theranostic opportunities and the possibility to engineer extracellular signaling. Here, we developed an optoproteomic technology termed LUX-MS that exploits singlet oxygen generators (SOG) for the light-triggered identification of acute protein interactions on living cells. Using SOG-coupled antibodies, small molecule-drugs, biologics and intact viral particles, we show that not only ligand-receptor interactions can be decoded across organisms, but also the surfaceome receptor nanoscale organization ligands engage in with direct implications for drug action. Furthermore, investigation of functional immunosynapses revealed that intercellular signaling inbetween APCs and CD8+ T cells can be mapped now providing insights into T cell activation with spatiotemporal resolution. LUX-MS based decoding of surfaceome signaling architectures provides unprecedented molecular insights for the rational development of theranostic strategies.

systems biology↗

bioRxiv2019

Gene-flow from steppe individuals into Cucuteni-Trypillia associated populations indicates long-standing contacts and gradual admixture

The Cucuteni-Trypillia complex (CTC) flourished in eastern Europe for over two millennia (5100 - 2800 BCE) from the end of the Neolithic to the Early Bronze Age. Its vast distribution area encompassed modern-day eastern Romania, Moldova and western/central Ukraine. Due to a lack of existing burials throughout most of this time, only little is known about of the people associated with this complex and their genetic composition. Here, we present genome-wide data generated from the skeletal remains of four females that were excavated from two Late CTC sites in Moldova (3500 - 3100 BCE). All individuals carried a large Neolithic-derived ancestry component and were genetically more closely related to Linear Pottery than to Anatolian farmers. Three of the specimens also showed considerable amounts of steppe-related ancestry, suggesting influx into the CTC gene-pool from people affiliated with, for instance, the Ukraine Mesolithic. The latter scenario is supported by archaeological evidence. Taken together, our results confirm that the steppe component had arrived in eastern Europe farming communities maybe as early as 3500 BCE. In addition, they are in agreement with the hypothesis of ongoing contacts and gradual admixture between incoming steppe and local western populations.

genomics↗