Biology subjects

Hofmann, N.

Publications and source records attributed to Hofmann, N..

7 recordsLinked to original sources

bioRxiv2026

Conserved cerebellar rhombic lip compartmentalization and Eomes regulatory networks govern unipolar brush cell development

The rhombic lip (RL) gives rise to all cerebellar glutamatergic cell types, including unipolar brush cells (UBCs). Disruptions to UBC development can lead to the neurodevelopmental disorder Dandy-Walker Syndrome and the pediatric brain tumor medulloblastoma, but these diseases have not been adequately modeled in mice. To evaluate conservation of UBC development in mouse and human, we examined UBC localization, lineage decisions, and the underlying molecular mechanisms of UBC differentiation using multiplex immunofluorescence and single-cell RNA-seq of wild-type and conditional knockout animals of the primary UBC transcription factor Eomes. Similar to the human RL, the murine RL is molecularly compartmentalized, cycling EOMES+ UBC progenitors are highly abundant, and persist after birth. Eomes regulates the transcriptional networks important for UBC differentiation and migration, but not UBC fate. Overall, our findings suggest that murine UBC development recapitulates many features of human UBC development, with EOMES playing a central role in UBC maturation.

developmental biology↗

bioRxiv2026

Accelerating multi-objective VHH discovery via integrated high-throughput selection and AlphaFold3-guided structure prediction

Discovering therapeutic antibodies that bind multiple related targets with high affinity and favourable biophysical properties remains challenging and resource intensive. For snakebite antivenoms, this challenge is critical as treatments must neutralise toxins across multiple snake species. We developed a pipeline combining high-throughput yeast screening, deep sequencing, and AlphaFold3 structure prediction to rapidly identify poly-specific variable domains of heavy-chain-only antibodies (VHHs) against long-chain -neurotoxins. Multiplexed yeast display screening generated a dataset of diverse candidates with varying binding specificities. AlphaFold3-generated VHH-toxin complex predictions enabled structure-based prioritisation that accurately predicted poly-specific binders targeting conserved epitopes across multiple toxins. These structural insights enabled computational optimisation of both affinity and solubility without disrupting target recognition. Experimental validation confirmed improved variants maintained broad specificity across toxins. This integrated approach accelerates multi-objective antibody discovery by predicting which candidates will bind multiple targets before extensive laboratory testing, providing a generalisable strategy applicable beyond antivenoms to any therapeutic requiring broad target coverage.

bioengineering↗

bioRxiv2025

Functionally distinct ALK and ROS1 fusions detected in infant-type hemispheric gliomas converge on STAT3 and SHP2 activation

ALK and ROS1 fusions are emerging as key drivers of infant-type hemispheric gliomas (IHG). With diverse gene partners, the impact of ALK and ROS1 oncoprotein heterogeneity on glioma biology remains unknown. We developed an integrative phospho-proteomic and transcriptomic approach to discover biological functions regulated by five IHG-associated fusions: CCDC88A::ALK, PPP1CB::ALK, GOPC::ROS1, CLIP1::ROS1 and KIF21A::ROS1. Here, we report fusion-specific oncogenic functions conferred by the 5 gene partner, including increased cell motility driven by microtubule-interacting fusions CCDC88A::ALK and CLIP1::ROS1. All studied fusions converged on a non-canonical STAT3 activation. Using affinity purification mass spectrometry, we identify SHP2 in direct interaction with all three ROS1 oncoproteins, but with none of the ALK oncoproteins, which in turn interact with SHC1/SHC3. ROS1 fusions phosphorylated SHP2 to a larger extent than ALK fusions, and analyses of downstream pathways suggested MAPK-independent, non-canonical SHP2-driven functions. Our findings reveal both common and fusion-specific dependencies, offering opportunities to optimize therapeutic strategies for pediatric gliomas.

cancer biology↗

bioRxiv2023

A Comparative Study of Protein Structure Prediction Tools for Challenging Targets: Snake Venom Toxins

Protein structure determination is a critical aspect of biological research, enabling us to understand protein function and potential applications. Recent advances in deep learning and artificial intelligence have led to the development of several protein structure prediction tools, such as AlphaFold2 and ColabFold. However, their performance has primarily been evaluated on well-characterised proteins, and comparisons using proteins with poor reference templates are lacking. In this study, we evaluated three modelling tools on their prediction of over 1000 snake venom toxin structures with no reference templates. Our findings show that AlphaFold2 (AF2) performed the best across all assessed parameters. We also observed that ColabFold (CF) only scored slightly worse than AF2, while being computationally less intensive. All tools struggled with regions of intrinsic disorder, such as loops and propeptide regions, and performed well in predicting the structure of functional domains. Overall, our study highlights the importance of exercising caution when working with proteins that have poor reference templates, are large, and contain flexible regions. Nonetheless, leveraging computational structure prediction tools can provide valuable insights into the modelling of protein interactions with different targets and reveal potential binding sites, active sites, and conformational changes, as well as into the design of potential molecular binders for reagent, diagnostic, or therapeutic purposes. StatementRecent advances in machine learning have led to the development of new protein structure prediction tools. However, these tools have mainly been tested on well-known proteins and their performance on proteins without known templates is unclear. This study evaluated the performance of three tools on over 1000 snake venom toxins. We found that while caution is required when studying poorly characterised proteins, these tools offer valuable opportunities to understand protein function and applications.

bioinformatics↗

bioRxiv2021

Converging evidence for differential regulatory control of APOEε4 on African versus European haplotypes

INTRODUCTIONThe difference in APOE{varepsilon}4 risk for Alzheimer disease (AD) between different populations is associated with APOE{varepsilon}4 local ancestry (LA). We examined LA SNPs with significant frequency differences between African and European/Japanese APOE{varepsilon}4 haplotypes for areas of differential regulation. METHODSWe performed two enhancer Massively Parallel Reporter Assay (MPRA) approaches, supplemented with single fragment reporter assays. We utilized Capture C analyses to support interactions with the APOE promoter. RESULTSThe TOMM40 intron 2 and 3 region showed increased enhancer activity in the European/Japanese versus African LA haplotypes in astrocytes and microglia. This region overlaps with APOE promoter interactions as assessed by Capture C analysis. Single variant analyses pinpoints rs2075650/rs157581, and rs59007384 as functionally different on these haplotypes. DISCUSSIONBoth differential regulatory function and Capture C data support an intronic region in TOMM40 as contributing to the differential APOE expression between African and European/Japanese LA.

genomics↗

bioRxiv2020

Inhibiting coronavirus replication in cultured cells by chemical ER stress

Coronaviruses (CoVs) are important human pathogens for which no specific treatment is available. Here, we provide evidence that pharmacological reprogramming of ER stress pathways can be exploited to suppress CoV replication. We found that the ER stress inducer thapsigargin efficiently inhibits coronavirus (HCoV-229E, MERS-CoV, SARS-CoV-2) replication in different cell types, (partially) restores the virus-induced translational shut-down, and counteracts the CoV-mediated downregulation of IRE1 and the ER chaperone BiP. Proteome-wide data sets revealed specific pathways, protein networks and components that likely mediate the thapsigargin-induced antiviral state, including HERPUD1, an essential factor of ER quality control, and ER-associated protein degradation complexes. The data show that thapsigargin hits a central mechanism required for CoV replication, suggesting that thapsigargin (or derivatives thereof) may be developed into broad-spectrum anti-CoV drugs. One Sentence Summary / Running titleSuppression of coronavirus replication through thapsigargin-regulated ER stress, ERQC / ERAD and metabolic pathways

immunology↗

bioRxiv2017

Development Of Amplicon Deep Sequencing Markers And Data Analysis Pipeline For Genotyping Multi-Clonal Malaria Infections

Amplicon deep sequencing permits sensitive detection of minority clones and improves discriminatory power for genotyping multi-clone Plasmodium falciparum infections. Such high resolution is needed for molecular monitoring of drug efficacy trials. Targeted sequencing of molecular marker csp and novel marker cpmp was conducted in duplicate on mixtures of parasite culture strains and 37 field samples. A protocol to multiplex up to 384 samples in a single sequencing run was applied. Software \"HaplotypR\" was developed for data analysis. Cpmp was highly diverse (He=0.96) in contrast to csp (He=0.57). Minority clones were robustly detected if their frequency was >1%. False haplotype calls owing to sequencing errors were observed below that threshold. To reliably detect haplotypes at very low frequencies, experiments are best performed in duplicate and should aim for coverage of >10000 reads/amplicon. When compared to length polymorphic marker msp2, highly multiplexed amplicon sequencing displayed greater sensitivity in detecting minority clones.

microbiology↗