Biology subjects

Hermann, L.

Publications and source records attributed to Hermann, L..

5 recordsLinked to original sources

bioRxiv2026

Interplay of NuA4/TIP60 and PRC2 Complex Activities in Fusion Driven Endometrial Stromal Sarcoma

Low-grade endometrial stromal sarcoma (LGESS) exhibits frequent chromosomal translocations that fuse various subunits of the NuA4/TIP60 co-activator complex to subunits of the Polycomb Repressive Complex 2 (PRC2) complex. LGESS fusion proteins, such as the commonly occurring JAZF1-SUZ12, have been shown to upregulate genes through mislocalization of NuA4/TIP60 activity to Polycomb target genes. In this study, we characterized an interesting recurrent fusion protein in LGESS that fused a NuA4/TIP60 component, MBTD1, to EZHIP. EZHIP is a recently described vertebrate protein that enzymatically inhibits methyltransferase activity of the PRC2 complex and is a potent oncogene. The MBTD1-EZHIP fusion protein forms a chimeric TIP60-PRC2.1 complex and drastically reduces H3K27me3 levels at Polycomb target genes, similar to EZHIP-overexpressing cancers. However, unlike EZHIP overexpression, MBTD1-EZHIP requires mislocalization of NuA4/TIP60 activity through the MBTD1 protein to upregulate oncogenes. Despite differences in the finer molecular mechanisms, MBTD1-EZHIP and the common JAZF1-SUZ12 fusion protein upregulated similar sets of genes in cell lines, showing a convergence of oncogenic gene expression. Surprisingly, unlike in cellular models, JAZF1-SUZ12 translocated patient samples showed not only upregulation of genes driven by increased H4K8ac and decreased H3K27me3 but also downregulation of specific genes due to accumulated H3K27me3, revealing an additional oncogenic mechanism in LGESS.

cancer biology↗

bioRxiv2026

Catabolite Activator Protein and quorum sensing cross-control group behaviors in Vibrio campbellii

Vibrio species adapt to different niches by sensing and responding to environmental signals such as nutrients, host cues, and quorum sensing autoinducers. Vibrio campbellii uses the master quorum sensing transcription factor LuxR to control expression of hundreds of genes at high cell density. Furthermore, many gamma-proteobacteria use the global transcription factor Catabolite Activator Protein (CAP) to control numerous physiologically relevant pathways, many of which are also modulated by quorum sensing, such as competence, biofilm formation, and carbon metabolism. However, the extent to which these two global transcription factors overlap to co-regulate gene expression and bacterial behaviors is understudied. In this work, we used ChIP-seq and RNA-seq to determine the individual and combined regulons of CAP and LuxR in V. campbellii. We found that CAP and LuxR co-occupied 11 promoters to synergistically or antagonistically co-regulate genes involved with metabolism, respiration, and virulence. It was previously proposed that CAP and LuxR both bound the bioluminescence (luxCDABE) promoter to co-regulate these genes, and our RNA-seq data showed that these were indeed the most strongly co-regulated genes. However, our ChIP-seq data revealed that only LuxR bound the luxCDABE promoter in vivo. This pattern of co-regulation--where both CAP and LuxR strongly impact transcription but only LuxR binds the promoter--was the most common mechanism observed. Our model for bioluminescence regulation is that CAP indirectly activates luxCDABE expression through the regulation of an intermediate factor. This study established new connections between the global gene regulatory networks underpinning nutrient sensing and population sensing. ImportanceVibrio bacteria (vibrios) colonize and infect diverse marine hosts including corals, fish, oysters, and shrimp, and can also cause life-threatening human infections, all of which are rising annually due to increasing ocean temperatures. To develop effective treatments against Vibrio infections, it is critical to understand the global gene regulation mechanisms vibrios use that enable pathogenic lifestyles. Signal transduction systems in bacteria are well-characterized; however, how vibrios coordinate global gene expression changes in response to multiple environmental inputs is understudied. Here, we determined how the aquaculture pathogen Vibrio campbellii regulates global gene expression in response to bacterial population signals and nutrient availability signals. Our findings help contextualize how vibrios respond to their fluctuating environments in nature.

microbiology↗

bioRxiv2025

Unveiling the temporal impact: Exploring dynamic changes in the paediatric solid tumour immune microenvironment through time

The composition of the tumour immune microenvironment (TIME) influences tumour evolution and responsiveness to immunotherapy. While longitudinal changes in TIME have been well-characterized in adult cancers, its dynamics in childhood cancers remain poorly documented, limiting our ability to predict treatment responses and tailor immunotherapeutic strategies. This study aimed to evaluate the plasticity of TIME in paediatric solid tumours, investigate its longitudinal evolution, and identify time-dependent immune alterations. Transcriptomic data from longitudinal samples of 27 paediatric patients (<21 years old) with relapsed or refractory solid tumours were analysed, encompassing 70 timepoints: 16 diagnoses and 54 successive relapses. TIME plasticity was assessed using gene expression clustering and immune cell infiltration enumeration. Patient-adjusted longitudinal analyses were performed using generalised linear mixed models (glmmSeq), adjusted for age and sex. Temporal associations of immune changes were further explored using dynamic regression models. Thirteen patients exhibited significant changes in their TIME profile, indicating high TIME plasticity. Over time, the TIME shifted toward a tolerogenic and immunosuppressive state, characterised by decreased activity in immune pathways (e.g., T cell receptor signalling) and enrichment of tolerogenic (e.g., macrophage differentiation) and oncogenic pathways (e.g., IL6-JAK-STAT3). The core enrichment of upregulated pathways contained key immunosuppressive factors: immune checkpoints (CTLA-4), tumour-associated macrophage activators (CSF1/CSF1R), T-regulatory cell activators (TGFB1), and immunosuppressive genes (IL10RA). This study provides evidence that the TIME in paediatric solid tumours is plastic and remodels towards immune depletion and tolerogenicity. This evolution may underlie treatment resistance and disease progression, underscoring the need for TIME-informed therapeutic approaches in paediatric oncology. Significance StatementThis article demonstrates the plasticity of the tumour immune micro-environment (TIME) of paediatric solid tumours throughout disease evolution. Longitudinal transcriptomic analyses of 70 tumour samples from 27 patients showed a progressive remodelling towards tolerogenicity and immune depletion. Key immunosuppressive factors, including immune checkpoints and tumour-associated macrophages, were identified as potential contributors to immune escape. These findings support the relevance of longitudinal immune monitoring in paediatric oncology and may inform future strategies for immunotherapeutic interventions.

cancer biology↗

bioRxiv2024

Beware of Data Leakage from Protein LLM Pretraining

Pretrained protein language models are becoming increasingly popular as a backbone for protein property inference tasks such as structure prediction or function annotation, accelerating biological research. However, related research oftentimes does not consider the effects of data leakage from pretraining on the actual downstream task, resulting in potentially unrealistic performance estimates. Reported generalization might not necessarily be reproducible for proteins highly dissimilar from the pretraining set. In this work, we measure the effects of data leakage from protein language model pretraining in the domain of protein thermostability prediction. Specifically, we compare two different dataset split strategies: a pretraining-aware split, designed to avoid similarity between pretraining data and the held-out test sets, and a commonly-used naive split, relying on clustering the training data for a downstream task without taking the pretraining data into account. Our experiments suggest that data leakage from language model pretraining shows consistent effects on melting point prediction across all experiments, distorting the measured performance. The source code and our dataset splits are available at https://github.com/tfiedlerdev/pretraining-aware-hotprot.

bioinformatics↗

bioRxiv2024

Multiple levels of transcriptional regulation control glycolate metabolism in Paracoccus denitrificans

The hydroxyacid glycolate is a highly abundant carbon source in the environment. Glycolate is produced by unicellular photosynthetic organisms and excreted at petagram scales to the environment, where it serves as growth substrate for heterotrophic bacteria. In microbial metabolism, glycolate is first oxidized to glyoxylate by the enzyme glycolate oxidase. The recently described {beta}-hydroxyaspartate cycle (BHAC) subsequently mediates the carbon-neutral assimilation of glyoxylate into central metabolism in ubiquitous Alpha- and Gammaproteobacteria. While the reaction sequence of the BHAC was elucidated in Paracoccus denitrificans, little is known about the regulation of glycolate and glyoxylate assimilation in this relevant alphaproteobacterial model organism. Here, we show that regulation of glycolate metabolism in P. denitrificans is surprisingly complex, involving two regulators, the IclR-type transcription factor BhcR that acts as an activator for the BHAC gene cluster, as well as the GntR-type transcriptional regulator GlcR, a previously unidentified repressor that controls the production of glycolate oxidase. Furthermore, an additional layer of regulation is exerted at the global level, which involves the transcriptional regulator CceR that controls the switch between glycolysis and gluconeogenesis in P. denitrificans. Together, these regulators control glycolate metabolism in P. denitrificans, allowing the organism to assimilate glycolate together with other carbon substrates in a simultaneous fashion, rather than sequentially. Our results show that the metabolic network of Alphaproteobacteria shows a high degree of flexibility to react to the availability of multiple substrates in the environment.

microbiology↗