Biology subjects

Hofer, M.

Publications and source records attributed to Hofer, M..

11 recordsLinked to original sources

bioRxiv2026

CATFISHR: integration of transcriptome and inferred CNV profiles for comprehensive malignant cell identification

Malignant cell identification in single-cell RNA sequencing (scRNA-seq) remains challenging because transcriptomic cell typing, somatic variant detection and inferred copy-number approaches each have modality-specific limitations. Rare or ambiguous malignant populations are especially vulnerable to misclassification or exclusion, despite their relevance to treatment resistance, minimal residual disease, and metastasis. We developed CATFISHR, a semi-automated workflow that integrates RNA-expression similarity, inferred copy-number variation (CNV) profiles, and consensus cell typing to classify malignant cells relative to high-confidence references. CATFISHR was evaluated across eight cohorts, including seven scRNA-seq datasets spanning multiple carcinomas and melanoma subtypes, and one 10x Visium spatial transcriptomics sample. Compared with available benchmarks or ground truths, CATFISHR achieved balanced accuracy > 0.85 in six of eight cohorts and F1 score > 0.80 in six of eight cohorts. Cells uniquely identified by CATFISHR as malignant ("Hidden" cells) were present in every dataset and were not consistently explained by standard quality-control metrics. In several cohorts, Hidden cells were transcriptionally closer to benchmark malignant than non-malignant compartments; in Visium data, sampled Hidden spots contained histologist-confirmed morphologically malignant cells. CATFISHR reduces missed malignant calls while preserving rare, transitional and benchmark-discordant populations for downstream investigation.

bioinformatics↗

bioRxiv2026

An epigenetic palimpsest: the King penguin's blood methylome reveals conserved hematopoietic ageing

Age-associated DNA methylation is conserved across vertebrates, but whether epigenetic ageing reflects cellular ageing programmes or age-dependent shifts in cell composition remains unresolved. Here, using 126 whole-blood methylomes from known-age King penguins (Aptenodytes patagonicus), we exploit a vertebrate system in which nucleated erythrocytes dominate peripheral blood, minimizing the influence of leukocyte heterogeneity. We identify a core set of 409 ageing-associated genes showing lifelong, clock-like methylation change. These genes are strongly enriched for regulators of hematopoietic stem and progenitor cell (HSPC) function and niche communication. Integration of methylome, transcriptome and chromatin-accessibility data reveals that many of the strongest ageing signals derive from genes inactive in mature erythrocytes, consistent with the persistence of epigenetic states from ancestral hematopoietic progenitors. A comparison with methylation profiles from 1,501 humans identified a conserved cross-species subset of ageing genes, and a human epigenetic age model constructed solely from orthologues of penguin ageing genes predicts chronological age with high accuracy while remaining largely insensitive to blood cell composition. We propose that blood epigenetic ageing signatures contain a long-lived cellular memory of stem-cell ageing, that may represent an evolutionarily ancient layer of the vertebrate ageing process.

systems biology↗

bioRxiv2026

The BEAC, an epigenetic clock for birds

Epigenetic clocks are powerful tools for estimating both chronological and biological age, enabling the integration of age information into population monitoring, demographic modelling, and research on the ecophysiology and evolution of ageing. Most epigenetic clocks so far have been developed for mammals: here, we present the Bird Epigenetic Ageing Clock (BEAC) for estimating chronological age in avian species. BEAC was established based on genome-wide enzymatic methylation sequencing data of known-age king penguins (Aptenodytes patagonicus), and validated in nine other bird species. The BEAC collects age-informative signals into a bisulfite amplicon sequencing panel of 24 primer pairs, providing a highly accurate and cost-effective alternative to sequencing-intensive approaches. It achieved strong predictive performance in independent king penguin training (R{superscript 2}=0.88; MAE=1.7 years, n=78) and testing data (R{superscript 2}=0.79; MAE=2.3 years, n=41), with negligible batch effects, high longitudinal consistency, and resilience to reduced sample size or missing loci. Importantly, cross-species validation across 180 samples showed that BEAC reliably captures age-associated methylation signals in nine additional bird species across seven clades, demonstrating that a single set of loci can be predictive of ageing across multiple different bird species. BEAC offers a flexible, empirically validated tool and a transferable framework for developing epigenetic clocks in avian species, providing a highly valuable resource for eco-evolutionary studies of ageing in wild species.

molecular biology↗

bioRxiv2025

A STAT5B-driven mouse model of hepatosplenic γδ T-cell lymphoma reveals therapeutic efficacy of JAK inhibition

Hepatosplenic T-cell lymphoma (HSTCL) is a rare and aggressive neoplasm associated with poor responses to standard chemotherapy regimens and low survival rates. No targeted therapies are available for HSTCL, and preclinical models to test new treatment options have not been established. The JAK-STAT signaling cascade is a key dysregulated pathway in HSTCL, and STAT5BN642His the most frequent somatic mutation in the disease. Here, we report on newly established clonal, murine {gamma}{delta} T-cell lymphoma cell lines initiated and driven by oncogenic STAT5BN642H, which recapitulate key immunophenotypic features, gene expression profiles and typically low cytolytic activity of patient-derived human HSTCL cells. CRISPR-Cas9 mediated knockout demonstrated growth dependence on STAT5BN642H. Murine C15 cells were allo-engrafted intravenously into both immunodeficient and immunocompetent mice to model an aggressive HSTCL-like disease at high penetrance, with recipient mice displaying hepatosplenomegaly and destructive {gamma}{delta} T cell organ infiltration, including bone marrow and blood involvement. We identified the potential of JAK inhibition as a targeted treatment strategy for HSTCL, and found the clinically approved JAK inhibitor upadacitinib to display selective anti-tumor efficacy against STAT5B-mutated HSTCL cell lines in vitro, in vivo, and in primary HSTCL patient samples. Overall, we describe the first robust STAT5B-driven preclinical model resembling features of HSTCL in an immune competent setting. This tool is expected to accelerate the study of HSTCL disease mechanisms and the testing of novel therapies. Our data further present the JAK inhibitor upadacitinib as a promising targeted treatment option for STAT5B-mutated HSTCL.

cancer biology↗

bioRxiv2025

Strain, procedures, and tools for reproducible genetic transformation and genome editing of Spirodela polyrhiza (L.) Schleid.

Duckweeds (Lemnaceae) have excellent potential for fundamental and applied research due to ease of cultivation, small size, and continuous fast clonal growth. However, their usage as model organisms and platforms for biotechnological applications is often limited by the lack of universal genetic manipulation methods necessary for transgene expression, gene editing, and other methods to modify gene expression. To identify suitable strains for genetic manipulation of the giant duckweed, Spirodela polyrhiza, we screened several genotypes for callus induction and regeneration and established genetic transformation. We have identified SP162 to be amenable to Agrobacterium-mediated transformation via tissue culture. The procedure is robust and reproducible across laboratories, allowing stable expression of different reporter genes and selectable markers, enabling CRISPR/Cas9-mediated genome editing. In addition, due to a weak small RNA-based silencing response, S. polyrhiza sustains prolonged periods of transgene activity in transient expression assays. To promote duckweed research and encourage the adoption of S. polyrhiza, we have made SP162 (ID#: 5676) and its genome publicly available and provide here detailed procedures for its cultivation and transformation. Furthermore, we created a web server to explore its genome, retrieve gene sequences, and implemented orthologous gene search and a gRNA design function for diverse CRISPR/Cas-based applications (https://agxu.uni-mainz.de/SP162/).

plant biology↗

bioRxiv2024

Aberrant iron deposition in the multiple sclerosis spinal cord relates to neurodegeneration

BackgroundIron accumulates in microglia-macrophages at the edge of multiple sclerosis (MS) lesions in the brain. Iron-rimmed brain lesions strongly predict disability accumulation, supporting iron metabolism is crucial in MS pathology. Little is known about iron distribution in the spinal cord. MethodsAutopsy cervical, thoracic and lumbar spinal cord samples from 9 controls and 46 MS donors of whom a subset (n=36) had mesiofrontal motor cortical tissue available for study, were labelled and systematically assessed for iron (DAB-enhanced Turnbull), myelin (PLP), axons (Palmgren silver), microglia-macrophages (TMEM119, Iba1, CD68), astroglia (GFAP), oligodendroglia (OLIG2), acute axonal injury (B-APP, SMI-32, NPY-1R) and oxidative stress (E06). MS lesional and non-lesional areas were considered. Total non-haem iron was quantified by inductively coupled plasma optical emission spectroscopy (ICP-OES). ResultsIn controls, iron predominantly localised to oligodendrocytes with total non-haem iron relating to total myelin fraction, which markedly differed in MS where iron accumulated in microglia-macrophages, subpial astrocytes, and axons in non-lesional areas. Iron laden microglia-macrophages were over-represented relative to total microglial-macrophages and displayed dysmorphic features. Iron-positive axons showed a disto-proximal gradient (highest at lumbar level) with a predilection for the corticospinal tracts. The extent of iron axon positivity related to smaller spinal cord area, lower total axonal counts, and greater oxidative stress. Iron positivity in each cellular compartment (i.e. subpial astrocytes, microglia-macrophage and axons) related to one-another and total non-haem iron correlated with axonal counts in MS. No iron-rimmed lesions were detected in the spinal cord unlike in cortical grey and subcortical white matter of the same cases where 22% and 80% of iron-rimmed lesions, respectively, were seen. ConclusionsDespite the conspicuous absence of iron-rimmed lesions in the MS spinal cord, we demonstrate widespread aberrant iron distribution in the MS spinal cord that relates to oxidative stress and neurodegeneration independent of demyelination. The distal cord predominant and corticospinal tract specific accumulation of iron in axons mirrors the pattern of length-dependent motoric disability commonly encountered in progressive MS. These findings implicate aberrant iron accumulation as a novel, clinically relevant, feature of MS spinal cord pathology.

neuroscience↗

bioRxiv2024

Locating the Missing Chlorophylls f in Far-red Photosystem I

The discovery of chlorophyll f-containing oxygenic photosynthesis, with its long-wavelength photochemistry, represented a new low-energy paradigm. However, subsequent structural studies on chlorophyll f-containing Photosystem I (PSI) found five chlorophylls f but none among the photochemically active pigments and concluded that chlorophyll f plays no photochemical role. Here we report a cryo-EM structure (2.01 [A]) of far-red PSI from Chroococcidiopsis thermalis PCC 7203, showing all eight chlorophylls f, including the redox active A-1B. Simulations of absorption difference spectra induced by charge separation indicate that the A-1B chlorophyll f absorbs at 755 nm. The chlorophyll f sites, some wavelength assignments, and conserved far-red-specific amino acids, provide functional insights, including redox tuning of chlorophyll f as the primary donor and far-red excitation energy-sharing over the PSI trimer.

biochemistry↗

bioRxiv2024

A Bioengineered Platform for Enhanced Observability of Patterned Gastrointestinal Organoid Monolayers with Bilateral Access

Studying the physiology and pathology of gastrointestinal (GI) tissues requires tools that can accurately mimic their complex architecture and functionality in vitro. Organoids have emerged as one such promising tool, though their closed structures with poorly accessible lumen and limited observability makes readouts challenging. In this study, we introduce a bioengineered organoid platform that generates bilaterally accessible 3D tissue models, allowing independent manipulation of both the apical and basal sides of patterned epithelial monolayers. We successfully constructed gastric, small intestinal, caecal, and colonic epithelial models that faithfully reproduce tissue-respective geometries and exhibit high physiological relevance, evidenced by the regionalization of stem cells and transcriptional resemblance to real epithelia. The gained observability allowed single-cell tracking over time and studies into the motility of cells in immersion and air-liquid interface cultures. Additionally, this model recapitulated Trichuris muris infection of the caecum epithelium, allowing the first live imaging of syncytial tunnel formation. Overall, this platform offers accessible organoids with improved observability, making it a valuable tool for investigating the dynamics of GI epithelial cells and their interactions with pathogens.

bioengineering↗

bioRxiv2021

Microarrayed human bone marrow organoids for modeling blood stem cell dynamics

In many leukemia patients, a poor prognosis is attributed either to the development of chemotherapy resistance by leukemic stem cells (LSCs) or to the inefficient engraftment of transplanted hematopoietic stem/progenitor cells (HSPCs) into the bone marrow (BM). Here, we build a 3D in vitro model system of bone marrow organoids (BMOs) that recapitulate several structural and cellular components of native BM. These organoids are formed in a high-throughput manner from the aggregation of endothelial and mesenchymal cells within hydrogel microwells. Accordingly, the mesenchymal compartment shows partial maintenance of its self-renewal and multilineage potential, while endothelial cells self-organize into an interconnected vessel-like network. Intriguingly, such a vascular compartment enhances the recruitment of HSPCs in a chemokine ligand/receptor-dependent manner, reminiscent of HSPC homing behavior in vivo. Additionally, we also model LSC migration and nesting in BMOs, thus highlighting the potential of this system as a well accessible and scalable preclinical model for candidate drug screening and patient-specific assays.

bioengineering↗

bioRxiv2019

StemBond hydrogels optimise the mechanical microenvironment for embryonic stem cells

Studies of mechanical signalling are typically performed by comparing cells cultured on soft and stiff hydrogel-based substrates. However, it is challenging to independently and robustly control both substrate stiffness and tethering of extracellular matrix (ECM) to substrates, making ECM tethering a potentially confounding variable in mechanical signalling investigations. Moreover, poor ECM tethering can lead to weak cell attachment. To address this, we developed StemBond hydrogels, a hydrogel formulation in which ECM tethering is stable and can be varied independently of stiffness. We show that soft StemBond hydrogels provide an optimal format for culturing embryonic stem (ES) cells. We find that soft StemBond substrates improve the homogeneity of ES cell populations, boost their self-renewal, and increase the efficiency of cellular reprogramming. Our findings underline how soft microenvironments impact mechanosensitive signalling pathways regulating self-renewal and differentiation, indicating that optimising the complete mechanical microenvironment will offer greater control over stem cell fate specification.

cell biology↗

bioRxiv2019

Exploring the space of human exploration

What drives peoples exploration in complex scenarios where they have to actively acquire information by making queries? How do people adapt their selection of queries to their environment? We explore these questions using Entropy Mastermind, a novel variant of the Mastermind code-breaking game, in which participants have to guess a secret code by making useful queries. Participants solved games more efficiently and more quickly if the entropy of the game environment was low; moreover, people adapted their initial queries to the scenario they were in. We also investigated whether it would be possible to predict participants queries within the generalized Sharma-Mittal information-theoretic framework. Although predicting individual queries is difficult, the modeling framework offered important insight on human behavior. Entropy Mastermind offers rich possibilities for modeling and behavioral research.

animal behavior and cognition↗