Biology subjects

Klein, K.

Publications and source records attributed to Klein, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Nose-to-Knee Transplantation for Osteochondral Regeneration: A Proof-of-Concept Study in Sheep Employing Ceramic-Hydrogel Osteochondral Grafts

Osteochondral defects remain a major clinical challenge, frequently progressing to osteoarthritis and ultimately requiring joint replacement. Despite advances in regenerative strategies, current approaches often fail to restore the structural and functional complexity of the osteochondral unit, resulting in poor integration and limited long-term performance. Here, we developed autologous osteochondral grafts combining mechanically mature nasal chondrocyte-derived cartilage with a 3D-printed strontium-hardystonite-gahnite trabecular bone scaffold, which was tested in an osteochondral defect model in sheep. Nasal chondrocytes were encapsulated in a hyaluronan transglutaminase-alginate hydrogel generating hyaline-like cartilage with physiologically relevant compressive properties (1.0 +/- 0.2 MPa) after 6 weeks of in vitro maturation. MicroCT scans of the osteochondral unit were used to design biomimetic trabecular bone scaffolds. Controlled infiltration of the hydrogel into the trabecular pores and subsequent cartilage maturation created a mechanical interlock between cartilage and bone layer, reaching an interfacial shear strength of 201 +/- 42 kPa. The translational potential of this approach was evaluated in a proof-of-concept ovine study. The engineered cartilage remained attached to the bone scaffold for three months following implantation, but osteochondral repair was limited by implant sinking, likely caused by inadequate implant fixation in the defect, resulting in micromotion, synovial fluid infiltration, osteolysis and subsequent bone cyst formation. Together, this work demonstrates the feasibility of engineering mechanically mature autologous osteochondral grafts while identifying subchondral bone integration as the primary bottleneck limiting successful osteochondral regeneration and future clinical translation.

bioengineering↗

bioRxiv2026

Direct anti-inflammatory actions of N,N-dimethyltryptamine on microglia are revealed by proteomic profiling and receptor pharmacology

N,N-dimethyltryptamine (DMT) is an endogenous psychedelic tryptamine that has recently emerged as a promising therapeutic candidate for acute ischemic stroke. Although DMT consistently reduces infarct size, attenuates neuroinflammation, and improves functional outcome in experimental stroke, the cellular and receptor mechanisms underlying these effects remain poorly understood. Primary rat microglial cultures were used to examine the direct anti-inflammatory effects of DMT following lipopolysaccharide (LPS)-induced activation. Microglial morphology, phagocytosis, and proteomic alterations were analyzed. Radioligand binding assays determined the affinity of DMT for microglial sigma-1 receptors (Sig-1Rs). Pharmacological inhibition of Sig-1Rs and serotonin (5-HT) receptors was performed to define receptor-specific mechanisms. Translational relevance was evaluated in acute mouse brain slices subjected to mild oxygen-glucose deprivation (mOGD) and anoxic episodes, where microglial activation, spreading depolarizations (SDs), and neuronal injury were assessed. DMT directly suppressed LPS-induced microglial activation, promoted a homeostatic morphology, and reduced phagocytic activity. Proteomic profiling demonstrated that DMT selectively reprogrammed inflammatory pathways by suppressing proteins involved in cytokine and chemokine signaling and oxidative stress while largely preserving arachidonic acid-prostaglandin synthesis. DMT bound microglial Sig-1Rs with micromolar affinity comparable to that reported in whole-brain preparations. Pharmacological inhibition revealed that DMT-induced morphological reprogramming required both Sig-1R and serotonergic signaling, whereas suppression of phagocytosis was largely independent of either receptor pathway. In acute brain slices, DMT attenuated microglial activation, reduced SD propagation and ischemic neuronal injury, and tissue-level neuroprotection depended on serotonergic signaling. DMT directly targets microglia and selectively remodels inflammatory states rather than broadly suppressing microglial activation. The receptor mechanisms underlying its actions are context dependent, with Sig-1R and serotonergic signaling contributing differentially according to the cellular response and experimental model. These findings provide mechanistic insight into the neuroprotective actions of DMT and support its ongoing clinical translation as a potential therapy for ischemic stroke.

neuroscience↗

bioRxiv2025

Investigation of CD36 interactome provides insights into multimolecular complexes necessary for anti-angiogenic signalling

Signal transduction is a fundamental process that enables cells to adapt to external cues and organize adequate responses including survival, death, growth, and homeostasis. A key mechanism modulating signal transduction relies on the formation of multimolecular complexes optimized for specificity, modularity and signal amplification. The scavenger receptor CD36, which binds diverse ligands in different cellular contexts, illustrates this principle. To uncover the nature of CD36 multimolecular complexes, we employed a proximity biotinylation labeling approach on human endothelial cells, where CD36 binds to thrombospondin-1 (TSP-1) to initiate a signaling cascade promoting programmed cell death. Using biotin capture and mass spectrometry protein identification, we uncovered a list of proteins in the vicinity of CD36. This list of candidates was refined by proximity ligation assays. The relationship between key CD36 interacting molecules, in particular active integrin beta-1 (ITGB1) and CD9, was further decoded by conditional colocalization analysis, providing support for their association within a tri-molecular complex. The implication of selected candidates in the signaling function of CD36 was further evaluated using shRNA knockdown, revealing that active ITGB1 is essential for Fyn activation downstream of CD36, with the tetraspanin playing a connecting role between CD36 and active ITGB1. Our approach to investigating CD36 complexes emphasizes the complexity and fundamental role of protein-protein interactions and coordination in the context of transmembrane signal transduction.

cell biology↗

bioRxiv2025

Why they occur here but not there - a case study of Great Spotted Woodpeckers in the city of Munich

O_LIMany animal species can occur in the urban environment. The factors determining whether a particular species can live in a particular place in the city are, however, often not known. Such knowledge is needed to be able to design a built environment that is suitable for species. C_LIO_LIThe Great Spotted Woodpecker, Dendrocopos major, breeds in self-made cavities in trees and regularly occurs in cities. Here, we used a number of approaches to elucidate the factors that influence the occurrence of woodpeckers in the build-up area of the city. C_LIO_LIWe studied the occurrence of D. major on 103 squares in Munich, Germany and linked their presence to a number of square features such as square size, position in the city, tree occurrences, and a number of other variables. We also observed the presence of woodpecker cavities and undertook behavioural observations to study tree use. C_LIO_LIWoodpeckers were observed on 60% of the squares. A random forest model showed that the number of humans on squares negatively affected woodpecker occurrence, while a number of tree-related variables, such as tree density, tree diversity, the number of old trees (>60 cm DBH), and the sum of DBH of trees on the square, positively affected occurrence. Some other variables were also important, such as the amount of green in the surroundings and the distance to the city centre. C_LIO_LINests were found only in trees with a DBH>20 cm, and there was a distinct preference for larger trees, whereby a range of species was accepted. Behavioural observations showed that woodpeckers used a wide variety of trees, including small ones. Particular species and trees with a DBH>20 cm are preferred. C_LIO_LIOur study shows that humans can design public places for the presence of the Great Spotted Woodpecker by providing a locally high abundance of trees of different species with total DBH close to 25m. Trees in the surroundings and the presence of softwood trees with >40 cm will make it more likely that woodpeckers will use such sites in the city. C_LI Statement on inclusionOur study brings both established scientists with permanent faculty positions with Ph.D.-students and students of the 2nd year of their B.Sc.-studies or 1st or 2nd year of their M.Sc.-studies for whom this work is the first experience in the publication of scientific results. Students were particularly encouraged to contribute to question and hypothesis development as well as analysis and interpretation.

ecology↗

bioRxiv2025

Langerhans Cell-targeted mRNA Delivery: A Strategy for Dose-Sparing and Enhanced Anti-Tumor Immunity

Despite the success of mRNA therapeutics, challenges remain in optimizing immune responses and minimizing side effects. Cell-specific antigen delivery may help reduce required doses and improve vaccine efficacy. In this study, we report on the first targeted delivery system for mRNA to a specific subset of skin-resident antigen-presenting cells - Langerhans cells. By functionalizing lipid nanoparticles (LNPs) with a langerin-specific glycomimetic ligand, we achieve selective mRNA delivery to both murine and human primary Langerhans cells with minimal off-target uptake, at the same time resulting in significantly increased mRNA translation. This targeted mRNA delivery not only enhances antigen presentation and T cell responses but also enables dose-sparing and superior anti-tumor immunity compared to conventional immunization in a B16-OVA tumor model. Importantly, our platforms high compatibility with various lipid nanoparticle formulations offers a flexible and precise tool for skin-directed mRNA delivery.

immunology↗

bioRxiv2025

Interactive delineation and quantification of anatomical structure with virtual reality

A virtual environment, equipped with suitable data representations, interaction techniques, and method interfaces, can facilitate effective human-in-the-loop analytics of 3D data. Motivated by this observation, we propose Brainacle, a native editor for the interactive delineation and quantification of anatomical structures in virtual reality. We validate this in a case study, where we process the gross brain regions of 20 individual animals from six different species of African cichlid fish from the tribe Lamprologinii, endemic to Lake Tanganyika in Africa. The software presented in this article can be used to quickly visualise and obtain an overview of imaged animal tissues, visually communicate features of interest, interactively add delineations, and perform different measurements in the same 3D environment. Brainacle is made available free of charge at https://brainacle.org and on the research data repository DaRUS.

bioinformatics↗

bioRxiv2025

Langerhans Cell-targeted Protein Delivery Enhances Antigen-Specific Cellular Immune Response

Targeted antigen delivery to immune cells, particularly dendritic cells, has emerged as a promising strategy to enhance therapeutic efficacy of vaccines, while minimizing adverse effects associated with conventional immunization. In this study, we use our previously described small glycomimetic molecule that selectively recognizes the Langerhans cell (LC)-specific surface receptor Langerin and demonstrate specific delivery of protein antigens to these specialized dendritic cells. Our results show that Langerin-mediated antigen delivery significantly enhances the immune response in vivo, resulting in increased expansion and activation of antigen-specific T cells, compared to immunization with unmodified antigen. We demonstrate the feasibility of our LC-targeted platform for immune cell-specific immunization with protein antigen and underscore the potential of LCs as an access point for next-generation vaccines and immunotherapies.

immunology↗

bioRxiv2025

Supramolecular assembly of collagen mimetic peptide D-periodic fibrils and nanoassemblies

The collagen triple helix assembles hierarchically into bundled oligomers, solvated networks and fibers. Synthetic peptide assemblies, driven by supramolecular interactions, can form single triple helices through intrahelical amino acid pairs, but the principles guiding interhelical associations into higher-order structures remain unclear. Here, we incorporate cation-{pi} and electrostatic charge pairs to probe interhelical interactions and elucidate the mechanisms driving triple helix assembly into fibrils, nanotubes, and nanosheets. Introducing cation-{pi} pairs into a fibrillating collagen mimetic resulted in D-periodic fibrils with pH-sensitive gelation. Modifying the presentation of interhelical interactions also enabled the characterization of another D-periodic fibril resembling cartilage collagens, featuring inner and outer triple helix layers. Enhancing electrostatic charge pairs promoted antiparallel assembly, leading to the formation of nanotubes and nanosheets. The packing behavior of triple helices correlates with the interhelical interactions, where parallel associations favor fibril formation, and antiparallel interactions drive nanotube and nanosheet assembly.

biochemistry↗

bioRxiv2025

MeTrEx: Membrane Trajectory Explorer

BackgroundMolecular Dynamics (MD) simulations provide valuable insights into the behaviour of biomolecules, particularly in complex systems such as cellular membranes. However, the increasing volume of MD data presents significant challenges in data visualisation, exploration and analysis. ResultWe present MeTrEx (Membrane Trajectory Explorer), a Python-based software designed to enhance the exploration and analysis of MD simulation data, with a focus on ligand and membrane molecule interactions. MeTrEx offers an intuitive graphical user interface for visualisation, advanced interaction tools, and comprehensive analytical capabilities. The software also supports comparative analyses of molecular trajectories and integrates external datasets for a more holistic view. A case study analysing the interaction of Polymyxin B1 with a bacterial membrane demonstrates the tools capabilities to investigate complex molecular behaviours. ConclusionBy combining detailed molecular analysis with interactive visualisation, MeTrEx provides researchers with a powerful platform to investigate complex biomolecular systems, contributing to a deeper understanding of ligand-membrane interactions.

bioinformatics↗

bioRxiv2024

5' HOXD Genes Differentially Regulate Gene Expression of Synovial Fibroblasts in Hand Joints

We previously demonstrated that Homeobox (HOX) transcription factors are differentially expressed between joint locations and can accurately assign synovial fibroblasts (SFs) to their correct joint location. We show here that the expression of the 5HOXD transcription factors HOXD10, HOXD11, and HOXD13 in SFs strikingly overlaps with predilection sites for the development of rheumatoid arthritis (RA). Changes in SFs gene expression after silencing 5HOXDs aligned with joint-specific differences of RA SFs. In particular, we identify HOXD13 as regulator or primary cilia function in SFs modulating cell cycle, DNA damage and proteasome activity. Accordingly, we show joint specific differences in primary cilia morphology, DNA damage repair and proteasome activity. We thus propose that HOXD13 and primary cilia play a role in shaping joint-specific SFs functions that might underlie the pathognomic pattern of joint involvement in RA.

cell biology↗

bioRxiv2024

Repurposing CD19-directed immunotherapies for pediatric t(8;21) acute myeloid leukemia

In contrast to patients with B cell precursor acute lymphoblastic leukemia (BCP-ALL), patients with acute myeloid leukemia (AML) have not yet benefited from recent advances in targeted immunotherapy. Repurposing immunotherapies that have been successfully used to target other hematological malignancies could, in case of a shared target antigen, represent a promising opportunity to expand the immunotherapeutic options for AML. Here, we evaluated the expression of CD19 in a large pediatric AML cohort, assessed the ex vivo AML killing efficacy of CD19-directed immunotherapies, and characterized the bone marrow immune microenvironment in pediatric AML, BCP-ALL, and non-leukemic controls. Out of 167 newly diagnosed de novo pediatric AML patients, 18 patients (11%) had CD19+ AML, with 61% carrying the translocation t(8;21)(q22;q22). Among CD19+ samples, we observed a continuum of CD19 expression levels on AML cells. In individuals exhibiting unimodal and high CD19 expression, the antigen was consistently present on nearly all CD34+CD38- and CD34+CD38+ subpopulations. In ex vivo AML-T cell co-cultures, blinatumomab demonstrated substantial AML killing, with an efficacy similar to BCP-ALL. In addition, CAR T cells could effectively eliminate CD19+ AML cells ex vivo. Furthermore, our immunogenomic assessment of the bone marrow immune microenvironment of newly diagnosed pediatric t(8;21) AML revealed that T- and NK cells had a less exhausted and senescent phenotype in comparison to pediatric BCP-ALL. Altogether, our study underscores the promise of CD19-directed immunotherapies for the treatment of pediatric CD19+ AML.

immunology↗

bioRxiv2024

Radioproteomics stratifies molecular response to antifibrotic treatment in pulmonary fibrosis

Antifibrotic therapy with nintedanib is the clinical mainstay in the treatment of progressive fibrosing interstitial lung disease (ILD). High-dimensional medical image analysis, known as radiomics, provides quantitative insights into organ-scale pathophysiology, generating digital disease fingerprints. Here, we used an integrative analysis of radiomic and proteomic profiles (radioproteomics) to assess whether changes in radiomic signatures can stratify the degree of antifibrotic response to nintedanib in (experimental) fibrosing ILD. Unsupervised clustering of delta radiomic profiles revealed two distinct imaging phenotypes in mice treated with nintedanib, contrary to conventional densitometry readouts, which showed a more uniform response. Integrative analysis of delta radiomics and proteomics demonstrated that these phenotypes reflected different treatment response states, as further evidenced on transcriptional and cellular levels. Importantly, radioproteomics signatures paralleled disease- and drug related biological pathway activity with high specificity, including extracellular matrix (ECM) remodeling, cell cycle activity, wound healing, and metabolic activity. Evaluation of the preclinical molecular response-defining features, particularly those linked to ECM remodeling, in a cohort of nintedanib-treated fibrosing ILD patients, accurately stratified patients based on their extent of lung function decline. In conclusion, delta radiomics has great potential to serve as a non-invasive and readily accessible surrogate of molecular response phenotypes in fibrosing ILD. This could pave the way for personalized treatment strategies and improved patient outcomes.

molecular biology↗

bioRxiv2023

The α-dystroglycan N-terminus is a broad-spectrum antiviral agent against SARS-CoV-2 and enveloped viruses

The COVID-19 pandemic has shown the need to develop effective therapeutics in preparedness for further epidemics of virus infections that pose a significant threat to human health. As a natural compound antiviral candidate, we focused on -dystroglycan, a highly glycosylated basement membrane protein that links the extracellular matrix to the intracellular cytoskeleton. Here we show that the N-terminal fragment of -dystroglycan (-DGN), as produced in E. coli in the absence of post-translational modifications, blocks infection of SARS-CoV-2 in cell culture, human primary gut organoids and the lungs of transgenic mice expressing the human receptor angiotensin I-converting enzyme 2 (hACE2). Prophylactic and therapeutic administration of -DGN reduced SARS-CoV-2 lung titres and protected the mice from respiratory symptoms and death. Recombinant -DGN also blocked infection of a wide range of enveloped viruses including the four Dengue virus serotypes, influenza A virus, respiratory syncytial virus, tick-borne encephalitis virus, but not human adenovirus, a non-enveloped virus in vitro. This study establishes soluble recombinant -DGN as a broad-band, natural compound candidate therapeutic against enveloped viruses.

microbiology↗

bioRxiv2023

A lineage-specific STAT5BN642H mouse model to study NK-cell leukemia

Patients with T- and NK-cell neoplasms frequently have somatic STAT5B gain-of-function mutations. The most frequent STAT5B mutation is STAT5BN642H, which is known to drive murine T-cell leukemia although its role in NK-cell malignancies is unclear. Introduction of the STAT5BN642H mutation into human NK-cell lines enhances their potential to induce leukemia in mice. We have generated a mouse model that enables tissue-specific expression of STAT5BN642H and have selectively expressed the mutated STAT5B in hematopoietic cells (N642Hvav/+) or exclusively in NK cells (N642HNK/NK). All N642Hvav/+ mice rapidly develop an aggressive T-/NK T-cell leukemia, whereas N642HNK/NK mice display an indolent chronic lymphoproliferative disorder of NK cells (CLPD-NK) that progresses to an aggressive leukemia with age. Samples from NK-cell leukemia patients have a distinctive transcriptional signature driven by mutant STAT5B, which overlaps with that of murine STAT5BN642H-expressing NK cells. We have generated the first reliable STAT5BN642H-driven pre-clinical mouse model that displays an indolent CLPD-NK progressing to aggressive NK-cell leukemia. This novel in vivo tool will enable us to explore the transition from an indolent to an aggressive disease and will thus permit the study of prevention and treatment options for NK-cell malignancies. Key pointsO_LIGeneration of a lineage-specific STAT5BN642H transgenic mouse model which develops NK-cell leukemia C_LIO_LILeukemic NK cells with a STAT5B gain of function mutation have a unique transcriptional profile in mice and human patients C_LI

cancer biology↗

bioRxiv2023

Elucidating the role of water in collagen self assembly by isotopically modulating collagen hydration

Water is known to play an important role in collagen self assembly, but it is still largely unclear how water-collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self assembly. We dissolve collagen in H2O and D2O, and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen-water interface, increasing the self assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions, which appear to be crucial in determining the acceleration of the initial nucleation rate. These results show that water acts as a mediator between collagen monomers, by moderating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self assembly.

biophysics↗

bioRxiv2023

Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics

The field of spatial transcriptomics is rapidly evolving, with increasing sample complexity, resolution, and tissue size. Yet the field lacks comprehensive solutions for automated integration and analysis of multi-slice data in either stacked (3D) or co-planar (2D) formation. To address this, we developed VR-Omics, a free, platform-agnostic software that distinctively provides end-to-end automated processing of multi-slice data through a biologist-friendly interface. Benchmarking against existing methods demonstrates VR-Omics unique strengths to perform comprehensive end-to-end analysis of multi-slice stacked data. Applied to rare paediatric cardiac rhabdomyomas, VR-Omics uncovered previously undetected dysregulated metabolic networks through co-planar slice analysis, demonstrating its potential for biological discoveries.

bioinformatics↗

bioRxiv2023

RIF1 regulates replication origin activity and early replication timing in B cells

The mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin, regulates early origin firing and promotes early replication. RIF1 has a minor role in gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal new layers of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.

molecular biology↗

bioRxiv2023

Evaluating Prompt Tuning for Conditional Protein Sequence Generation

Designing artificial proteins with specialized functions promises new solutions for biological, medical, and environmental use cases. This field benefits from advances in natural language processing, with state-of-the-art text generation models already being successfully applied to protein sequences. Openly available pre-trained protein language models are able to generate artificial protein sequences and can be finetuned on very specific tasks. Considering the high computational cost of finetuning a model exclusively for one downstream task, prompt tuning has been proposed as a more cost-efficient alternative that shares one model across different tasks. However, no openly available implementation of this approach compatible with protein language models has been previously published. Thus, we adapt an open-source codebase designed for NLP models to build a pipeline for prompt tuning on protein sequence data, supporting the protein language models ProtGPT2 and RITA. We benchmark this implementation for generating proteins of a specific family and evaluate the approach using text processing metrics as well as family membership prediction and protein activity prediction of generated sequences. Our results confirm the advantages of prompt tuning in resource usage, especially storage, encouraging further research and expansion of this technique to related use cases. For our evaluated use case, prompt tuning does not reach up to finetuning in terms of the quality of generated protein sequences, indicating the need for more extensive optimization. Lastly, we observe discrepancies between results of similar evaluation tools, highlighting open problems for principled assessment of protein sequence generation quality.

bioinformatics↗