Biology subjects

Luginbuehl, J.

Publications and source records attributed to Luginbuehl, J..

5 recordsLinked to original sources

bioRxiv2025

TP53 and RB1 are predictive genetic biomarkers for sensitivity to cytarabine in gliomas

Therapeutic progress in glioma, one of the most lethal human cancers, has been limited by molecular heterogeneity and lack of biomarker-driven drug deployment. Here we used a proprietary large-scale CRISPRi screening in primary patient-derived glioma tumorspheres to identify genetic vulnerabilities and nominate pharmacologically tractable targets. DNA polymerase-linked dependencies emerged as top-ranked hits, which we validated through orthogonal viability assays. Network-based integration of dependency data with drug-target relationships nominated cytarabine, a nucleoside analogue already approved for intrathecal use, as a candidate agent targeting this axis. Dose-response profiling across molecularly diverse glioma models revealed substantial heterogeneity in cytarabine sensitivity (IC50 range: 0.04-9.8 {micro}M). Machine learning analysis of whole-genome sequencing data identified TP53 wild-type and RB1-wild-type status as dominant predictors of response, with double wild-type lines showing three standard deviations (3 s.d.) increased sensitivity compared to altered models. Prospective validation in an independent cohort confirmed that TP53/RB1 genotype stratifies cytarabine activity. These findings establish a mechanistically anchored, biomarker-restricted repurposing opportunity for cytarabine in leptomeningeal glioma, enabling rational prioritisation of an accessible therapy in a molecularly defined patient subset.

cancer biology↗

bioRxiv2025

A human cell-free translation screen identifies the NT-2 mycotoxin as a ribosomal peptidyl transferase inhibitor

Translation inhibitors are invaluable for probing ribosome function and therapeutic applications, but systematic discovery in human systems is limited by the lack of scalable, screening-compatible cell-free platforms. Here, we establish a robust high-throughput screening using human lysates that bypasses cellular cytotoxic effects. After screening [~]28,000 small molecules, we identified known and a novel translation inhibitor, including NT-2, a trichothecene mycotoxin produced by the pathogenic Fusarium sporotrichioides. NT-2 suppressed protein synthesis in human cells and yeast lysates, while sparing translation in bacteria and intact yeast cells. Cryo-EM at 1.76 [A] revealed NT-2 bound at the peptidyl transferase center of the human 60S ribosome, confirming NT-2 as a ribosomal inhibitor associated with ribosomes in an inactive eEF2/SERBP1-associated dormant state. Together, these results expose NT-2 as a previously unrecognized environmental inhibitor of mammalian protein synthesis and demonstrate the power of cell-free translation screening to reveal new inhibitors with unexpected ribosome fates.

biochemistry↗

bioRxiv2024

Uncoupling the functional roles of Coronavirus Nsp1

When host cells are infected with coronaviruses, the first viral protein produced is Nsp1. This protein inhibits host protein synthesis and induces host mRNA degradation to enhance viral proliferation. Despite its critical role, the mechanism by which Nsp1 mediates cellular mRNA degradation remains unclear. In this study, we use cell-free translation to address how the host mRNA stability is regulated by Nsp1. We reveal that SARS-CoV-2 Nsp1 binding to the ribosome is enough to trigger mRNA degradation independently of ribosome collisions or active translation. MERS-CoV Nsp1 inhibits translation without triggering degradation, highlighting mechanistic differences between the two Nsp1 counterparts. Nsp1 and viral mRNAs appear to co-evolve, rendering viral mRNAs immune to Nsp1-mediated degradation in SARS-CoV-2, MERS-CoV and Bat-Hp viruses. By providing new insights into the mode of action of Nsp1, our study helps to understand the biology of Nsp1 better and find new strategies for therapeutic targeting against coronaviral infections. SignificanceO_LICell-free assays allow the decoupling of Nsp1-mediated translation inhibition from RNA degradation. C_LIO_LINsp1 interaction with the ribosome is crucial for mRNA degradation, but active translation is not required. C_LIO_LISARS-CoV-2 Nsp1 induces mRNA degradation, while MERS-CoV Nsp1 inhibits translation without triggering degradation. C_LIO_LI5UTR-specific protection of viral mRNAs from Nsp1 indicates a co-evolutionary adaptation between the two features C_LI

molecular biology↗

bioRxiv2020

Non-allelic homologous recombination of Alu and LINE-1 elements generates somatic complexity in human genomes.

Millions of Alu and L1 copies in our genomes contribute to evolution and genetic disorders via non-allelic homologous recombination, but the somatic extent of these rearrangements has not been systematically investigated. Here we combine short and long DNA reads sequencing of repeat elements with a new bioinformatic pipeline to show that somatic recombination of Alu and L1 elements is common in human genomes. We report new tissue-specific recombination hallmarks, and show that retroelements acting as recombination hotspots are enriched in centromeres and cancer genes. We compare recombination profiles in human induced pluripotent stem cells and differentiated neurons and show that neuron-specific recombination of repeat elements accompanies chromatin changes during cell-fate determination. Finally, we find that somatic recombination profiles are altered in Parkinsons and Alzheimers disease, indicating a link between retroelements recombination and genomic instability in neurodegeneration. This work shows that somatic recombination of repeat elements contributes massively to genomic diversity in health and disease.

genomics↗

bioRxiv2019

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodelling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed. However, they still present some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a technology that maps genome-wide RNA-chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation-based methodology that reduces the bias for nascent transcription, while increasing genomic coverage and unique mapping rate efficiency compared to existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and emphasizes the role of transcription in the establishment of chromatin structure.

genomics↗